RetrogeneDB ID: retro_ecab_506

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:109880355..109881465(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002313
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TRAM1
• Ensembl ID: ENSECAG00000018378
• Aliases: None
• Description: translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]

Sequence

>retro_ecab_506
ATGGCGTTCCGTAAGAAGAGCCCCAGGAACCCCCCAGTCCTGAGCCACGAATTCATCCTGCAGAATCATGCAGACCTCGT
CGCCTGCGTGGGGATGTTCTTCGTGCTGGGGCTCATGTTCGAGGGAGCAGCAGAAGCATCTATCGTGTTTATTACTCTGC
AGCACAGCGTTACCTTCCCCGCGGCAGAAGAACCAGCCACGGACTTAAAGGTCCTTTATCATTATGGCATCAAAGATCTG
GCCACGGTTTTCTTCTACATGCTCGTGGCAATCATCATTCACGCCACCCTTCAGGAGTATGTGTTGGACAAAATTAACAG
GCGAATGCAGTTTCCCAAAGCGAAACAAAGCAGATTTAACGAATCTGGTCAGTTGAGTGCATTCTACCTTGTCTCTTGTA
TTTGGGGCACGTTCATTCTGATCTCTGAAAACTGCCTGTCGGACCCCACTCTCTTATGGGAGGCGCATTACCATAACGTG
ATGACGTTTCAGATGAAGTTTTTCTATATCTCACAGTTGGCTTACTGGTTTCATGCCTTTCCTGAACTCTACTTCCAGAG
AACGAAAAAACAAGACATCCCCCGTCAGCTTGTCTACATTGGGCTTCACCTCTTTCACATCGCCGGAGCCTATCTCCTGT
ACTTGAATCATCTGGGACTTGTTCTCCTGATGATGCATTACTTTGTTGAATTACTTTCCCACATTTGCGACCTGTTTTAT
TTTAGTGATGAAAAGTACCAGAAAGACATTTCTCTGTGGGCAATTGTGTTTATTTTGGGTCGACTTGTGACTTTAATTGT
CTCCGTGCTCGCTGTGGGCTTTCACCTGGCTGGAGGGCAGAATCGGAATCCCGATGCCGTCACCGGAAACGTGAATGTGT
TGGCAGCCAAAATTGCCGTTCTGTCGTCCAGTTGCACTATCCAAGCCTATATAACATGGAATTTATTTAATGTCCAGCTT
CAGAGGTGGATGGAAGAAGATGCTACTCTTCAGGCCCCAAGTGTGAAGAAGAAACGGACTAAAGGCAGGTCTTCCAGAAA
AGGAACAGAAAATGGGGTGGCAACGTCAAGTAGAGTAGACTCTCCGCATAAGAGGAAAGAGAAATCTTCA

Alignment

ORF - retro_ecab_506 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIRKKSSKSPPVLSHEFILQNHADIVSCVAMVFLLGLMFEITAKASIIFVTLQYNVTLPATEEQATESA
          MA.RKKS...PPVLSHEFILQNHAD.V.CV.M.F.LGLMFE..A.ASI.F.TLQ..VT.PA.EE.AT...
Retrocopy MAFRKKSPRNPPVLSHEFILQNHADLVACVGMFFVLGLMFEGAAEASIVFITLQHSVTFPAAEEPATDLK

Parental  SLYYYGIKDLATVFFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFSCIWGTFIL
          .LY.YGIKDLATVFFYMLVAIIIHA..QEYVLDKINRRM.F.K.K.S.FNESGQLSAFYL.SCIWGTFIL
Retrocopy VLYHYGIKDLATVFFYMLVAIIIHATLQEYVLDKINRRMQFPKAKQSRFNESGQLSAFYLVSCIWGTFIL

Parental  ISENYISDPTILWRAYPHNLMTFQMKFFYVSQLAYWFHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
          ISEN..SDPT.LW.A..HN.MTFQMKFFY.SQLAYWFHAFPELYFQ.TKK.DIPRQLVYIGL.LFHIAGA
Retrocopy ISENCLSDPTLLWEAHYHNVMTFQMKFFYISQLAYWFHAFPELYFQRTKKQDIPRQLVYIGLHLFHIAGA

Parental  YLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
          YLL.LNHLGLVLL..HYFVE.L.HI..LFYFSDEKYQK..SLWA..F.LGRL.TLI.SVL.VGF.LA...
Retrocopy YLLYLNHLGLVLLMMHYFVELLSHICDLFYFSDEKYQKDISLWAIVFILGRLVTLIVSVLAVGFHLAGGQ

Parental  NQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSA-FQAPAVKKKPTVTKGRSSRKG
          N...D..TGN.NVLA..IAVL.S.C..QA...W...N.QL.RW.E..A..QAP.VKKK...TKGRSSRKG
Retrocopy NRNPDAVTGNVNVLAAKIAVLSSSCTIQAYITWNLFNVQLQRWMEEDATLQAPSVKKKR--TKGRSSRKG

Parental  TENGVNGTVTSNGADSPRNRKEKSS
          TENGV....TS...DSP..RKEKSS
Retrocopy TENGV---ATSSRVDSPHKRKEKSS

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	2.72 RPM	89.14 RPM
SRP021940_cerebellum	8.36 RPM	15.94 RPM
SRP021940_embryo	12.04 RPM	27.26 RPM
SRP021940_placental_villous	2.02 RPM	147.36 RPM
SRP021940_synovial_membrane	5.30 RPM	44.20 RPM
SRP021940_testis	1.85 RPM	157.49 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_506 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_506 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_15

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006325	1 retrocopy	retro_amel_78,
Bos taurus	ENSBTAG00000007562	1 retrocopy	retro_btau_24,
Canis familiaris	ENSCAFG00000007866	1 retrocopy	retro_cfam_15,
Callithrix jacchus	ENSCJAG00000007893	1 retrocopy	retro_cjac_168,
Dasypus novemcinctus	ENSDNOG00000009296	2 retrocopies	retro_dnov_27, retro_dnov_906,
Dipodomys ordii	ENSDORG00000001901	1 retrocopy	retro_dord_27,
Equus caballus	ENSECAG00000018378	1 retrocopy	retro_ecab_506 ,
Echinops telfairi	ENSETEG00000018447	1 retrocopy	retro_etel_674,
Felis catus	ENSFCAG00000028775	1 retrocopy	retro_fcat_136,
Homo sapiens	ENSG00000067167	1 retrocopy	retro_hsap_51,
Loxodonta africana	ENSLAFG00000011625	1 retrocopy	retro_lafr_9,
Macaca mulatta	ENSMMUG00000001516	1 retrocopy	retro_mmul_235,
Mustela putorius furo	ENSMPUG00000010616	1 retrocopy	retro_mputfur_558,
Mus musculus	ENSMUSG00000025935	1 retrocopy	retro_mmus_117,
Nomascus leucogenys	ENSNLEG00000011376	1 retrocopy	retro_nleu_73,
Oryctolagus cuniculus	ENSOCUG00000008734	1 retrocopy	retro_ocun_52,
Otolemur garnettii	ENSOGAG00000006379	1 retrocopy	retro_ogar_2932,
Pongo abelii	ENSPPYG00000018660	1 retrocopy	retro_pabe_169,
Pan troglodytes	ENSPTRG00000020334	1 retrocopy	retro_ptro_2081,
Rattus norvegicus	ENSRNOG00000007892	1 retrocopy	retro_rnor_287,
Sus scrofa	ENSSSCG00000006193	1 retrocopy	retro_sscr_980,
Ictidomys tridecemlineatus	ENSSTOG00000005537	1 retrocopy	retro_itri_38,
Tarsius syrichta	ENSTSYG00000013887	1 retrocopy	retro_tsyr_24,
Tursiops truncatus	ENSTTRG00000000328	1 retrocopy	retro_ttru_24,