RetrogeneDB ID: retro_cfam_2176

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:67060373..67061831(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000017412
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ETS1
• Ensembl ID: ENSCAFG00000010304
• Aliases: None
• Description: v-ets avian erythroblastosis virus E26 oncogene homolog 1 [Source:HGNC Symbol;Acc:3488]

Sequence

>retro_cfam_2176
ATGAGCTACTTTGTGGATTCTGCAGCCAGTGGCCCTGCCCCTTATTCAGCAGTGCGGCCTGCTGTGGTGAGGCAGGGGCC
TATCAACTCCTATGAAGATCCTCAAATGGCCGGCCTGTGGTTTCCAGTCCAATTATCACCAGCAAAGAGCTTACTACCCC
TTCTGGGATAAGATAGCAACTCAGGAAGTTCCCACAGGTCTGGAACACTGTGGCCCAGATATGGAATGTGCTGATGTACC
ACTGTTAACTCCAAGCAGCAAAGAAATGATGTCTCAAGCATTGAAAGCTACTTTCAGTGGTTTCTCTAAAGAACAACAAA
GACTGGGAATTCCAAAAGACCCCCGGCAGTGACAGAAACCCATGTTCAGGACTGGATGATGTGGGCTGTGAATGAGTTCA
GCCTGAAAGGTATGGACTTCCAGAAGTTCTGTGTGAATGGGGCAGCCCTCTGCGCACTAGGAAAAGACTGCTTTCTCGAG
CTGGCCCCAGACTTCGTTGGGGATATCTTTTGGGAACATCTTGAGATCCTACAGAAAGAGAATGTGATACCATACCAAGT
GAATGGAGTCAACCCTACCTATCCAGAATCCCGCTATACCTCAGATTACTTCATTAGTTATGGTATGGAGCATGCTCAGT
GCGTTCCTTCCTCTGAGTTCTCAGAGCCTAGCTTCATCACAGAGTCCAACCAGACACTCCATCCCATTAGCTCGGAGGAA
CTCCTCTCCCTCACGTATGAGAATGACTACTCCTCGGTCATTCTCTGGGACCCTCTGCAGACAGACACCTTGCAGACTGA
CTACTTTGCCATCAAACAAGAAGTTGTAACCCCAGACAACATGTGCATGGGGAGGACCAGTTGTGATAAGCTCGGGGCCC
AGGACTCTTTTGAGAGTGTGGAGAGCTACGACAGTTGTGACTGCCTCACCCAGTCCCGGAGCAGCCATTCATCTTTTAGT
AGCCTGCAGCACATCCCCTCCTATGAAAGCGTCGACTCAGAGGACTATCCAGCTGCCCTGCCCAACCACAAGCCCAAGGG
CACCTTCAAGGACTATGTGCGTGACCATGCTGACCTCAACAAGGGCAAACCTATCATTCCTGCTGCTGCCCTGGCTGGCT
ACACAGGCAGTGGACCAATCCAGCTATGGCAGTTTCTTCTGGAATTACTCACTGATAAATCCTGTCAGTCTTTTATCAGC
TGGGTAGGAGATGGCTGGGAGTTCAAGCTTTCTGACCCAGAAGAGGTGGCCAGGAGATGGGGAAAAAGGAAAAACAAACC
TAAGATGAATTATGAGAAACTGAGCTGTGGCCTATGCTACTATTATGACAAAAACATCATCCAAGAAACAGCGAGTAAGC
GCTATGTGTACCGCTTTGTGTGTGACCTGCAGAACCTCCTGGGCTACACGCCCGAGGAACTCCACACCATGCTGGACATC
AAGCCCGATGCTGATGAG

Alignment

ORF - retro_cfam_2176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSYFVDSAASGPAPYSAVRPAVVRQGPINSYEDPRMA-CGFQSNYHPQRAYYP-FWDEMATQEVPTGLEH
          MSYFVDSAASGPAPYSAVRPAVVRQGPINSYEDP.MA...F.....P.....P.FWD..ATQEVPTGLEH
Retrocopy MSYFVDSAASGPAPYSAVRPAVVRQGPINSYEDPQMAGLWFPVQLSPAKSLLP>FWDKIATQEVPTGLEH

Parental  CGSDMECADVPLLTPSSKEMMSQALKATFSGFSKEQQRLGIPKDPRQ-WTETHVRDWVMWAVNEFSLKGV
          CG.DMECADVPLLTPSSKEMMSQALKATFSGFSKEQQRLGIPKDPRQ..TETHV.DW.MWAVNEFSLKG.
Retrocopy CGPDMECADVPLLTPSSKEMMSQALKATFSGFSKEQQRLGIPKDPRQ<VTETHVQDWMMWAVNEFSLKGM

Parental  DFQKFCMNGAALCALGKDCFLELAPDFVGDILWEHLEILQKEDVKPYQVNGVNPTYPESRYTSDYFISYG
          DFQKFC.NGAALCALGKDCFLELAPDFVGDI.WEHLEILQKE.V.PYQVNGVNPTYPESRYTSDYFISYG
Retrocopy DFQKFCVNGAALCALGKDCFLELAPDFVGDIFWEHLEILQKENVIPYQVNGVNPTYPESRYTSDYFISYG

Parental  IEHAQCVPPSEFSEPSFITESYQTLHPISSEELLSLKYENDYPSVILRDPLQTDTLQTDYFAIKQEVVTP
          .EHAQCVP.SEFSEPSFITES.QTLHPISSEELLSL.YENDY.SVIL.DPLQTDTLQTDYFAIKQEVVTP
Retrocopy MEHAQCVPSSEFSEPSFITESNQTLHPISSEELLSLTYENDYSSVILWDPLQTDTLQTDYFAIKQEVVTP

Parental  DNMCMGRTSRGKLGGQDSFESVESYDSCDRLTQSWSSQSSFNSLQRVPSYDSFDSEDYPAALPNHKPKGT
          DNMCMGRTS..KLG.QDSFESVESYDSCD.LTQS.SS.SSF.SLQ..PSY.S.DSEDYPAALPNHKPKGT
Retrocopy DNMCMGRTSCDKLGAQDSFESVESYDSCDCLTQSRSSHSSFSSLQHIPSYESVDSEDYPAALPNHKPKGT

Parental  FKDYVRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVAR
          FKDYVRD.ADLNK.KP.IPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISW.GDGWEFKLSDP.EVAR
Retrocopy FKDYVRDHADLNKGKPIIPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISWVGDGWEFKLSDPEEVAR

Parental  RWGKRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVKPDADE
          RWGKRKNKPKMNYEKLS.GL.YYYDKNII..TA.KRYVYRFVCDLQ.LLGYTPEELH.MLD.KPDADE
Retrocopy RWGKRKNKPKMNYEKLSCGLCYYYDKNIIQETASKRYVYRFVCDLQNLLGYTPEELHTMLDIKPDADE

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	0.00 RPM	10.46 RPM
SRP017611_brain	0.00 RPM	14.53 RPM
SRP017611_kidney	0.00 RPM	26.41 RPM
SRP017611_liver	0.00 RPM	31.91 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2176 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010304	1 retrocopy	retro_cfam_2176 ,
Canis familiaris	ENSCAFG00000013420	1 retrocopy	retro_cfam_1414,