RetrogeneDB ID: retro_ecab_1010

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 9:44953503..44954443(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL2L13
• Ensembl ID: ENSECAG00000010335
• Aliases: None
• Description: BCL2-like 13 (apoptosis facilitator) [Source:HGNC Symbol;Acc:17164]

Sequence

>retro_ecab_1010
ATGGCATCTTCTACTACTGTGCCTCTAGGGTTTCACTAGCATGAAAGTACAAAGTATGTTGTTCTCAGCTACTTGGGAGT
CTTCTCTCAGGAGAAGCTGCAAGAGCCACGTCTTTCCTCACCCCAAGGAGTTCAACAAGATGTAGCTTCACAATCTCTGA
TCAAGAAGTTTTATTAAAAGTTAAAACTGAAATTGAATAAGAGCTAAAATCTCTGGACAAAGAAATTTCTGAAGCCTTCA
CTAGCACAGGCTTTGACCCAGTCACACATCTCCAGTTTTGAACCTTGCTAACCCAGAAAGCTCAGTAGAAGATTGCTTGA
CTCATCTTCAAGAAAAAGTGTTGCAGGAACTGAAAGAGGCTCCACATGAGGAGCTGCTAATGCTCCTCAGCCAACCAGTG
ACATATCAGGCATATCAGGAATGTACACTGGAGACCACATTTCATGCCAGTGGCTGGAGTAAGATTTTGGTGTCTCTGAT
TTTGCTAGACAAATGCTTTTGGAGTTGACAAGACCTCATCAAGAACCTTTGTGTGCCATGCTGCAGTTTGATGTGATGTA
TCTGGAGGACTATGTAGCATAGTACATTATTCAGCAAAGTGGCTGGGGCACTGTCTTTAATTTTGAGTCAGAGGAGGAGG
AATATCCTGGAATCGTTGCAGAAGGTAGGAATGACACTTACATCCTGCCCAGTGACAACTCTGGACAAGTCAGTCCTCCA
GAGTCTCCAACTATGACCACTTTTTGGCAATCAGAGAGCTTACCTGTTTCACTGTCAGCCAGCAAGAGTTGGCACACAGA
AAAGCCTACCAGTGTCCCTAGGTCCTGAGTCCTGGCAGCAGATTGCAATGGATCTTAAAGAAGTCAAAAGCTTAGATAGC
AATAGGGCTGGAGAGAAGAGTGAGGATAATTCATCTAGTCCTGACATTTGCATGCTGGAG

Alignment

ORF - retro_ecab_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.25 %
• Parental protein coverage: 70.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MASSTTVPLGFH--YETKYVVLSYLGLLSQEKLQEQHLSSPQGVQQDVTSQTL-DQEVLLKVKAEIEEEL
          MASSTTVPLGFH....TKYVVLSYLG..SQEKLQE..LSSPQGVQQDV.SQ.L.DQEVLLKVK.EIE.EL
Retrocopy MASSTTVPLGFH*HESTKYVVLSYLGVFSQEKLQEPRLSSPQGVQQDVASQSL<DQEVLLKVKTEIE*EL

Parental  KSLDKEISEAFTTTGFDRHTS-PVFSPANP-ESSVEDCLAHLGEKVSQELKEPLQKALQMLLSQPVTYQA
          KSLDKEISEAFT.TGFD..T....F.P..P.ESSVEDCL.HL.EKV.QELKE.....L.MLLSQPVTYQA
Retrocopy KSLDKEISEAFTSTGFDPVTH>SSFEPC*P>ESSVEDCLTHLQEKVLQELKEAPHEELLMLLSQPVTYQA

Parental  YRECTLETTVHANGWNKILVPLILL-RQMLLELTRRGQEPLSALLQFGVTYLEDYAAEYIIQQGGWGTVF
          Y.ECTLETT.HA.GW.KILV.LILL.RQMLLELTR..QEPL.A.LQF.V.YLEDY.A.YIIQQ.GWGTVF
Retrocopy YQECTLETTFHASGWSKILVSLILL<RQMLLELTRPHQEPLCAMLQFDVMYLEDYVA*YIIQQSGWGTVF

Parental  NLESEEEEYPGTVAEDSNDIYILPSDNSGQVSPPESPTVTTSWQSESLPVSLSASQSWHTE-SLPVSLGP
          N.ESEEEEYPG.VAE..ND.YILPSDNSGQVSPPESPT.TT.WQSESLPVSLSAS.SWHTE.SLPVSLGP
Retrocopy NFESEEEEYPGIVAEGRNDTYILPSDNSGQVSPPESPTMTTFWQSESLPVSLSASKSWHTE>SLPVSLGP

Parental  ESWQQIAMDPEEVKSLDSNGAGEKSENNSSNSDIVHVE
          ESWQQIAMD..EVKSLDSN.AGEKSE.NSS..DI...E
Retrocopy ESWQQIAMDLKEVKSLDSNRAGEKSEDNSSSPDICMLE

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	18.71 RPM
SRP021940_cerebellum	0.00 RPM	27.42 RPM
SRP021940_embryo	0.00 RPM	39.74 RPM
SRP021940_placental_villous	0.00 RPM	42.10 RPM
SRP021940_synovial_membrane	0.00 RPM	25.48 RPM
SRP021940_testis	0.00 RPM	55.12 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1010 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1010 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1010 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010335	1 retrocopy	retro_ecab_1010 ,
Otolemur garnettii	ENSOGAG00000002830	1 retrocopy	retro_ogar_430,
Rattus norvegicus	ENSRNOG00000012394	1 retrocopy	retro_rnor_429,