RetrogeneDB ID: retro_ecab_1109

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:45521074..45521841(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSECAG00000016813
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_ecab_1109
GACCTCTGCCCTAACGTCACCTAGGACCTCGTGAAAGAGCTCAATGCCTCATCAGAGCTCTTGGTGATGGAGGTGGAGAT
GGAGGTGTACACCACGCTGAAACAGTGGATGTTCTTGCAGCTGCAGCCGACATGGAGGGGCCCCACAGAGCCCTATTGCC
CGAGGCCGACTTGTGGTTTGCCAGGTCCAGGAGGGAATAGGAGGGAGCTCCTTTCCTGGAGACCGAGGAGGGCAGAGCCT
TCGTGCCAGTGTTCCAGCAGCTGCGGCTCGCCTACATAATCTGTGACCTACCTTCAGCGCATATCATCGACCAGGATGCT
CTGATCCCTGCCTCATGGGTGACCCCAGTGTACAAAGAGCAGTGGCTTACCTTCCTCCGGGCTGAGCAGACCAGGGAGCT
CGGGCCGGTGGACGTCTACGTGTCCGACCCGCGGCAGAACAGCATGTGATGCGGTGGCCAGCTCCACAGGGATGAGCAGT
GCAGCTGGCGATGGAATGGCTTCAACTTCGGCTGGGACCTGGTGGTGTGCTACACCAACCGGCGCATCGTTTTCCGGCGC
AGCGTGCTGAACAAGTCCTGCGGCCTCGGGGTCAGCTTACTCTGGCAGAGAAAGGTCACATTCCGCCTGCGCCTGGCCTC
CTTGGACAGGGCTGGAAGAGCCGTTTTCAGGAAGGACACAGAATACCAGATGCTTTCCCTGAGAAAGGATCGAGAGCTAG
AGGTAGTGAACCTGGAGAATCAAGATGTGGTCTTCCCCATATATGTA

Alignment

ORF - retro_ecab_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.58 %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELFKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVPSWNGSL-KQLLTETDVWFSKRRKDFEG
          .L.........K.L..SS.L.VM.VEM.VYT.LK.WMFLQL.P.W.G.....LL.E.D.WF...R...EG
Retrocopy DLCPNVT*DLVKELNASSELLVMEVEMEVYTTLKQWMFLQLQPTWRGPT<RALLPEADLWFARSRRE*EG

Parental  MTFLETEQGKPFVSVFRHLRLQYIISDLASARIIEQDSLVPSEWLSSVYKQQWLAMLRAEQDSEVGPQEI
          ..FLETE.G..FV.VF..LRL.YII.DL.SA.II.QD.L.P..W...VYK.QWL..LRAEQ..E.GP...
Retrocopy APFLETEEGRAFVPVFQQLRLAYIICDLPSAHIIDQDALIPASWVTPVYKEQWLTFLRAEQTRELGPVDV

Parental  NKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFR
          .......NSM.CG..L..D....WRW.GFNFG.DL.V.YTNR.I.F.R..LN..C...VSL...R...FR
Retrocopy YVSDPRQNSM*CGGQLHRDEQCSWRWNGFNFGWDLVVCYTNRRIVFRRSVLNKSCGLGVSLLWQRKVTFR

Parental  LRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFPLYI
          LRLAS.D..G.......T.YQ.L.L.KD.E..V.NL......FP.Y.
Retrocopy LRLASLDRAGRAVFRKDTEYQMLSLRKDRELEVVNLENQDVVFPIYV

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
SRP021940_articular_cartilage	0.00 RPM	1.48 RPM
SRP021940_cerebellum	0.00 RPM	1.30 RPM
SRP021940_embryo	0.00 RPM	3.17 RPM
SRP021940_placental_villous	0.00 RPM	1.64 RPM
SRP021940_synovial_membrane	0.00 RPM	1.04 RPM
SRP021940_testis	0.00 RPM	76.92 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1109 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109 , retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,