RetrogeneDB ID: retro_ocun_876

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:52623632..52624450(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM19
• Ensembl ID: ENSOCUG00000012539
• Aliases: None
• Description: transmembrane protein 19 [Source:HGNC Symbol;Acc:25605]

Sequence

>retro_ocun_876
GCTTTCTGGATTATGTGAATGATAGCAAGCACCTGTTATGGTAATTTACGGCCAATTTCTCCTTGGCGTTGGCTGTTTTC
TGTTCCTGTTGTGATTGTCTCTAATGGCATTAAAAAGAAAAGTCTGGATCACAGTGGGGCTCTCGGAGGGTGAGTGGTTG
GATTTATGTTAACCATTGCAAATTTCAGTTTCTTTACCTCTTTGCTTATGTTTTTCATTTCTTCTTCAAAACTTACTAAA
TGGAAAGGAGAAACAAAGAAGTGTCTAGATTCAGAATGAAAGGAAGGTGGGCAAAAGAATTGGGTTCAGGTATTCTGTAA
TGGTGCCGTGCCTACAGAGCTGACCCTGCCATTCATGACAGAAAATGGCCCCAGGGAAATCCCAATTGATTTCTCCAAGC
AGTACACTGCTTCCTGGATGTGTTTGTCTCTTTTGGCTGCGCTGGCCTGCTCTGCTGGAGACATGTGGGCTTCGGAAGTT
GGCCAGGTTCTGAGTAAAAGCCCACCAAGACTGATAACAACCTGGAAGAAAGTTCCCATTGGGACAAATGGAGAAGTTAC
CATGGTGGACCTTGCTCCAGTCTCTTTGGTAGTACCTTTGTGGGCATCACATACTTCTTTACACAGTTGGTTTTTTGTGA
ATGATTTAGACATATCTGCTCCCCAGTGACCAATTATTGCATTTGGGGGTACAGCTATGTTACTAGATCAATTGTGGACT
CGTATTTAGGAGCAACAATGCAATTTTCAGGGTTGGATGAAAGCACTGGCATGGTAATCAATAGCCCAACAAATGAGGCA
AAGCACATATCAGGGAAA

Alignment

ORF - retro_ocun_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.33 %
• Parental protein coverage: 71.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AFWIMSMTASTYYGNLRPISPWRWLFSVVVPVLIVSNGIKKKSLDHSGALGGLVVGFILTIANYSFFTSL
          AFWIM.M.AST.YGNLRPISPWRWLFSV..PV.IVSNGIKKKSLDHSGALGG.VVGF.LTIAN.SFFTSL
Retrocopy AFWIM*MIASTCYGNLRPISPWRWLFSV--PVVIVSNGIKKKSLDHSGALGG*VVGFMLTIANFSFFTSL

Parental  LMFFLSSSKLTKWKGETKKRLDSEYKEGGQRNWVQVFCNGAVPTELALLFMIENGPGEIPIDFSKQYTAS
          LMFF.SSSKLTKWKGETKK.LDSE.KEGGQ.NWVQVFCNGAVPTEL.L.FM.ENGP.EIPIDFSKQYTAS
Retrocopy LMFFISSSKLTKWKGETKKCLDSE*KEGGQKNWVQVFCNGAVPTELTLPFMTENGPREIPIDFSKQYTAS

Parental  WMCLSLLAALACSAGDTWASEVGPVLSKSPPRLITTWKKVPVGTNGGVTMVGLA-SSLLGGTFVGLAYFL
          WMCLSLLAALACSAGD.WASEVG.VLSKSPPRLITTWKKVP.GTNG.VTMV.LA.SSL.G.TFVG..YF.
Retrocopy WMCLSLLAALACSAGDMWASEVGQVLSKSPPRLITTWKKVPIGTNGEVTMVDLA<SSLFGSTFVGITYFF

Parental  TQLI-FVNDLDLSAPQWPIIAFGGIAGLLG-SIVDSYLGATMQFSGLDETTGMVVNSPTNEAKHISGK
          TQL..FVNDLD.SAPQ.PIIAFGG.A.LL..SIVDSYLGATMQFSGLDE.TGMV.NSPTNEAKHISGK
Retrocopy TQLV>FVNDLDISAPQ*PIIAFGGTAMLLD<SIVDSYLGATMQFSGLDESTGMVINSPTNEAKHISGK

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
SRP017611_brain	0.06 RPM	56.46 RPM
SRP017611_kidney	0.00 RPM	55.04 RPM
SRP017611_liver	0.00 RPM	59.50 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_876 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_876 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
Oryctolagus cuniculus	ENSOCUG00000012539	1 retrocopy	retro_ocun_876 ,
Sarcophilus harrisii	ENSSHAG00000001776	1 retrocopy	retro_shar_761,