RetrogeneDB ID: retro_cfam_837

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:7878401..7879508(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSCAFG00000003081
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_cfam_837
ATGAACGTGGCCGCCAAGTACCGCCAGGCGTCCCTGTACGTGGGGGATCTCGACGCCGAGGTCACCGAGGACGCGCTGTT
CCGGAAGTTCAGCGCCGCGGGGCCCGTGCTGTCCATCCGCATCTGCAGGGACCTGCTGACCCGCCGCTCGCTGGGCTACG
CCTACGTGAACTTCCTGCGGCTGGCGGACGCGCAGCGGGCCCTGGACACCATGAACTTCGACGTGCTGCGGGGCCGGCCG
CTCCGCCTCATGTGGTCCCAGCGCGACGCGCACCTGCGGAAGTCGGGCGTCGGGAACGTGTTCATCAAGAACCTGGACCG
GTCCGTGGACGACAAGGCCCTCTTCGAGCGCTTCTCGGCCTTCGGGAAGATCCTGTCGTCCAAGGTGGTGAGCGACGAGC
GCGGCTCCCGCGGCTACGCGTTCGTGCACTTCCAGGAGCAGAGCGCCGCCGACCGCGCCATCGAGCACATGAACGGGGCG
CAGCTCCGCGGCTGCAGGCTCTTCGTGGGCCGCTTCCAGAGCCGCCAGGCCCGCGAGGCCGAGCTGCGCAGCCGCGCCGG
CGAGTTCACCAACCTGTACATCAAGAACTTCGGCGGCCGCATGGACGACGCCAGGCTCAGGGCCGTGTTCAGCGAGTACG
GCAAGACCCTGAGCGTCAAGGTGATGACCGACGCCAGCGGCAGGTCCCGCGGCTTCGGCTTCGTGAGCTTCGAGAGCCAC
GAGGCGGCCCGGCGGGCGGTGGAGGCCCTGAACGGCAGGCAGGTGGACGGGCAGCCGCTGTTCGTGGGCCGCGCGCAGAG
GAAGGCGGAGCGGCAGGCGGAGCTCAGGCGGGCCTTCGAGCAGCGGCAGCAGGACGGGCTCCGCAGGGCCCAGGGCGCCA
AGCTCTACGTCAAGAACCTGGACGACGCCGTCGACGAGGACAGGCTGCGCAGGGAGTTTTCTGGCTTCGGAGCCGTCAGC
AGGGTCAAGATCATGCGGGAGGAAGGGCGGAGCAAAGGCTTTGGCCTCATCTGCTTCTCCTCTGCCGACGAGGCCGCCAG
GGCCTTGGCCGAGATGAACGGCCGCGTGCTGGGCTCCAAGCCGCTGTCCATCGCCCTGGCCCAGAGG

Alignment

ORF - retro_cfam_837 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.68 %
• Parental protein coverage: 58.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.AA..Y..ASLYVGDL...VTE..L..KFS.AGPVLSIR.CRD..TRRSLGYAYVNF...ADA.RALD
Retrocopy MNVAAK-YRQASLYVGDLDAEVTEDALFRKFSAAGPVLSIRICRDLLTRRSLGYAYVNFLRLADAQRALD

Parental  TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDV..G.P.R.MWSQRD..LRKSGVGNVFIKNLD.S.D.KAL...FSAFG.ILS.KVV.DE.GS.GY
Retrocopy TMNFDVLRGRPLRLMWSQRDAHLRKSGVGNVFIKNLDRSVDDKALFERFSAFGKILSSKVVSDERGSRGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL
          AFVHF..Q.AAD.AIE.MNG..L.....FVGRF.SR..REAEL...A.EFTN.YIKNFG...DD..L...
Retrocopy AFVHFQEQSAADRAIEHMNGAQLRGCRLFVGRFQSRQAREAELRSRAGEFTNLYIKNFGGRMDDARLRAV

Parental  FSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKF
          FS..GKTLSVKVM.D.SG.S.GFGFVS.E.HE.A..AVE..NG....G...FVGRAQ.K.ERQAEL.R.F
Retrocopy FSEYGKTLSVKVMTDASGRSRGFGFVSFESHEAARRAVEALNGRQVDGQPLFVGRAQRKAERQAELRRAF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQ..Q....R.QG..LY.KNLDD..D...LR.EFS.FG.....K.M.E.GRSKGFG..CFSS..EA..A.
Retrocopy EQRQQDGLRRAQGAKLYVKNLDDAVDEDRLRREFSGFGAVSRVKIMREEGRSKGFGLICFSSADEAARAL

Parental  TEMNGRIVGSKPLYVALAQR
          .EMNGR..GSKPL..ALAQR
Retrocopy AEMNGRVLGSKPLSIALAQR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.71 RPM	34.77 RPM
SRP017611_brain	0.32 RPM	23.10 RPM
SRP017611_kidney	0.46 RPM	40.15 RPM
SRP017611_liver	0.44 RPM	49.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_837 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_837 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_109
Pan troglodytes	retro_ptro_2093
Gorilla gorilla	retro_ggor_2127
Pongo abelii	retro_pabe_2563
Callithrix jacchus	retro_cjac_214
Rattus norvegicus	retro_rnor_175

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837 ,
Canis familiaris	ENSCAFG00000018353	1 retrocopy	retro_cfam_1972,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,