Hi all,
I have following sample input file which is a part of big file:
ID AINX_HUMAN Reviewed; 499 AA.
AC Q16352; B1AQK0; Q9BRC5;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2002, sequence version 2.
DT 28-NOV-2012, entry version 123.
DE RecName: Full=Alpha-internexin;
DE Short=Alpha-Inx;
DE AltName: Full=66 kDa neurofilament protein;
DE Short=NF-66;
DE Short=Neurofilament-66;
DE AltName: Full=Neurofilament 5;
GN Name=INA; Synonyms=NEF5;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND VARIANT SER-92.
RC TISSUE=Fetal brain;
RX MEDLINE=95287809; PubMed=7769995;
RA Chan S.-O., Chiu F.-C.;
RT "Cloning and developmental expression of human 66 kd neurofilament
RT protein.";
RL Brain Res. Mol. Brain Res. 29:177-184(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15164054; DOI=10.1038/nature02462;
RA Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L.,
RA Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K.,
RA Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L.,
RA Taylor A., Battles J., Bird C.P., Ainscough R., Almeida J.P.,
RA Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J.,
RA Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J.,
RA Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D.,
RA Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S.,
RA Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L.,
RA Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S.,
RA Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L.,
RA Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J.,
RA Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M.,
RA Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S.,
RA Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M.,
RA Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A.,
RA Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T.,
RA Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I.,
RA Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T.,
RA Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M.,
RA Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W.,
RA Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H.,
RA Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L.,
RA Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K.,
RA Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T.,
RA Doucette-Stamm L., Beck S., Smith D.R., Rogers J.;
RT "The DNA sequence and comparative analysis of human chromosome 10.";
RL Nature 429:375-381(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Brain;
RX PubMed=15489334;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP PROTEIN SEQUENCE OF 46-83; 105-111; 121-130; 139-145; 216-228;
RP 279-288; 323-330; 339-367; 378-397 AND 407-430, AND MASS SPECTROMETRY.
RC TISSUE=Brain, Cajal-Retzius cell, and Fetal brain cortex;
RA Lubec G., Afjehi-Sadat L., Chen W.-Q., Sun Y.;
RL Submitted (DEC-2008) to UniProtKB.
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-496, AND MASS
RP SPECTROMETRY.
RC TISSUE=Embryonic kidney;
RX PubMed=17525332;
RA Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III,
RA Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N.,
RA Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J.;
RT "ATM and ATR substrate analysis reveals extensive protein networks
RT responsive to DNA damage.";
RL Science 316:1160-1166(2007).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-290, AND MASS SPECTROMETRY.
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.,
RA Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [8]
RP VARIANT [LARGE SCALE ANALYSIS] GLN-110.
RX PubMed=16959974; DOI=10.1126/science.1133427;
RA Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D.,
RA Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S.,
RA Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J.,
RA Dawson D., Willson J.K.V., Gazdar A.F., Hartigan J., Wu L., Liu C.,
RA Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N.,
RA Vogelstein B., Kinzler K.W., Velculescu V.E.;
RT "The consensus coding sequences of human breast and colorectal
RT cancers.";
RL Science 314:268-274(2006).
CC -!- FUNCTION: Class-IV neuronal intermediate filament that is able to
CC self-assemble. It is involved in the morphogenesis of neurons. It
CC may form an independent structural network without the involvement
CC of other neurofilaments or it may cooperate with NF-L to form the
CC filamentous backbone to which NF-M and NF-H attach to form the
CC cross-bridges.
CC -!- TISSUE SPECIFICITY: Found predominantly in adult CNS.
CC -!- DEVELOPMENTAL STAGE: Expressed in brain as early as the 16th week
CC of gestation, and increased rapidly and reached a steady state
CC level by the 18th week of gestation.
CC -!- PTM: O-glycosylated (By similarity).
CC -!- PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
CC -!- SIMILARITY: Belongs to the intermediate filament family.
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DR EMBL; S78296; AAB34482.1; -; mRNA.
DR EMBL; AL591408; CAI16744.1; -; Genomic_DNA.
DR EMBL; CH471066; EAW49653.1; -; Genomic_DNA.
DR EMBL; BC006359; AAH06359.1; -; mRNA.
DR IPI; IPI00001453; -.
DR PIR; I52658; I52658.
DR RefSeq; NP_116116.1; NM_032727.3.
DR UniGene; Hs.500916; -.
DR ProteinModelPortal; Q16352; -.
DR SMR; Q16352; 90-241, 259-329, 333-402.
DR IntAct; Q16352; 3.
DR STRING; Q16352; -.
DR PhosphoSite; Q16352; -.
DR DMDM; 20141266; -.
DR PaxDb; Q16352; -.
DR PeptideAtlas; Q16352; -.
DR PRIDE; Q16352; -.
DR DNASU; 9118; -.
DR Ensembl; ENST00000369849; ENSP00000358865; ENSG00000148798.
DR GeneID; 9118; -.
DR KEGG; hsa:9118; -.
DR UCSC; uc001kws.3; human.
DR CTD; 9118; -.
DR GeneCards; GC10P105026; -.
DR HGNC; HGNC:6057; INA.
DR HPA; CAB002059; -.
DR HPA; HPA008057; -.
DR MIM; 605338; gene.
DR neXtProt; NX_Q16352; -.
DR PharmGKB; PA29867; -.
DR eggNOG; NOG149366; -.
DR HOGENOM; HOG000230977; -.
DR HOVERGEN; HBG013015; -.
DR InParanoid; Q16352; -.
DR KO; K07608; -.
DR OMA; ASSYRKV; -.
DR OrthoDB; EOG4R5031; -.
DR PhylomeDB; Q16352; -.
DR GenomeRNAi; 9118; -.
DR NextBio; 34171; -.
DR ArrayExpress; Q16352; -.
DR Bgee; Q16352; -.
DR CleanEx; HS_INA; -.
DR Genevestigator; Q16352; -.
DR GermOnline; ENSG00000148798; Homo sapiens.
DR GO; GO:0005883; C:neurofilament; TAS:ProtInc.
DR GO; GO:0005200; F:structural constituent of cytoskeleton; TAS:ProtInc.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0007399; P:nervous system development; IEA:UniProtKB-KW.
DR GO; GO:0060052; P:neurofilament cytoskeleton organization; IEA:Compara.
DR GO; GO:0042246; P:tissue regeneration; IEA:Compara.
DR InterPro; IPR016044; F.
DR InterPro; IPR001664; IF.
DR InterPro; IPR006821; Intermed_filament_DNA-bd.
DR InterPro; IPR018039; Intermediate_filament_CS.
DR PANTHER; PTHR23239; PTHR23239; 1.
DR Pfam; PF00038; Filament; 1.
DR Pfam; PF04732; Filament_head; 1.
DR PROSITE; PS00226; IF; 1.
PE 1: Evidence at protein level;
KW Acetylation; Coiled coil; Complete proteome; Developmental protein;
KW Differentiation; Direct protein sequencing; Glycoprotein;
KW Intermediate filament; Neurogenesis; Phosphoprotein; Polymorphism;
KW Reference proteome.
FT CHAIN 1 499 Alpha-internexin.
FT /FTId=PRO_0000063783.
FT REGION 1 87 Head.
FT REGION 88 408 Rod.
FT REGION 88 129 Coil 1A.
FT REGION 130 142 Linker 1.
FT REGION 143 238 Coil 1B.
FT REGION 239 262 Linker 2.
FT REGION 263 408 Coil 2.
FT REGION 409 499 Tail.
FT COMPBIAS 449 454 Poly-Glu.
FT MOD_RES 72 72 Phosphoserine (By similarity).
FT MOD_RES 290 290 N6-acetyllysine.
FT MOD_RES 335 335 Phosphoserine (By similarity).
FT MOD_RES 496 496 Phosphoserine.
FT VARIANT 92 92 T -> S (in dbSNP:rs1063455).
FT /FTId=VAR_049808.
FT VARIANT 110 110 E -> Q (in a breast cancer sample;
FT somatic mutation).
FT /FTId=VAR_036369.
FT VARIANT 149 149 D -> H (in dbSNP:rs1063456).
FT /FTId=VAR_033497.
FT CONFLICT 37 41 GFRSQ -> ASVE (in Ref. 1; AAB34482).
FT CONFLICT 67 67 R -> A (in Ref. 1; AAB34482).
FT CONFLICT 128 132 ALRQR -> RCDT (in Ref. 1; AAB34482).
FT CONFLICT 141 141 E -> Q (in Ref. 1; AAB34482).
FT CONFLICT 147 152 LRDLRA -> PRHLP (in Ref. 1; AAB34482).
FT CONFLICT 191 198 GAERALKA -> RRARLKR (in Ref. 1;
FT AAB34482).
FT CONFLICT 244 244 A -> R (in Ref. 1; AAB34482).
FT CONFLICT 263 263 S -> A (in Ref. 1; AAB34482).
FT CONFLICT 301 301 S -> T (in Ref. 1; AAB34482).
FT CONFLICT 310 311 EE -> DQ (in Ref. 1; AAB34482).
FT CONFLICT 318 318 Missing (in Ref. 1; AAB34482).
SQ SEQUENCE 499 AA; 55391 MW; 4C972764E9E68D3E CRC64;
MSFGSEHYLC SSSSYRKVFG DGSRLSARLS GAGGAGGFRS QSLSRSNVAS SAACSSASSL
GLGLAYRRPP ASDGLDLSQA AARTNEYKII RTNEKEQLQG LNDRFAVFIE KVHQLETQNR
ALEAELAALR QRHAEPSRVG ELFQRELRDL RAQLEEASSA RSQALLERDG LAEEVQRLRA
RCEEESRGRE GAERALKAQQ RDVDGATLAR LDLEKKVESL LDELAFVRQV HDEEVAELLA
TLQASSQAAA EVDVTVAKPD LTSALREIRA QYESLAAKNL QSAEEWYKSK FANLNEQAAR
STEAIRASRE EIHEYRRQLQ ARTIEIEGLR GANESLERQI LELEERHSAE VAGYQDSIGQ
LENDLRNTKS EMARHLREYQ DLLNVKMALD IEIAAYRKLL EGEETRFSTS GLSISGLNPL
PNPSYLLPPR ILSATTSKVS STGLSLKKEE EEEEASKVAS KKTSQIGESF EEILEETVIS
TKKTEKSNIE ETTISSQKI
the expected output is to fetch entries: AC entries and CC entries infront of which -!- is present with FUNCTION. It should print only the sentences in FUNCTION before the next -!- entries come.
AC Q16352; B1AQK0; Q9BRC5;
CC -!- FUNCTION: Class-IV neuronal intermediate filament that is able to self-assemble. It is involved in the morphogenesis of neurons. It may form an independent structural network without the involvement of other euro filaments or it may cooperate with NF-L to form the filamentous backbone to which NF-M and NF-H attach to form the cross-bridges.
Please let me know relevant shell scripting. I tried awk and sed it doesnt work.