RetrogeneDB ID: retro_ocun_1940

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:77134624..77135844(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023763
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ST7L
• Ensembl ID: ENSOCUG00000000269
• Aliases: None
• Description: suppression of tumorigenicity 7 like [Source:HGNC Symbol;Acc:18441]

Sequence

>retro_ocun_1940
ATGTCAGAATGCAAGGTATGGAGAAACCCTCTAAACCTTTACAGAGGAGCAGAATATAGGAGATACACATGGGTGACCGG
TAAAGAGCCGCTTACATACTATGACATGAACTTGTCGGCTCAGGACCATCAGACCCTTTTCACCGGTGACACAGACATCC
TACGTCCTTCAGACACAGTTATGCAGAAGGCATGGAGGGAAAGAAATCCTCCAGCGCGAATCAAAGCAGCCTATCAAGCT
TTAGAATTAAACAATGACTGTGCCACTGCATACGTTCTACTGGCTGAGGAAGAAGCAACAACCATTGTAGATGCTGAAAG
ATTATTTAAGCAGGCACTCAAAGCAGGAGAAACAATTTATAGGCGGTCACAGCAGTGCCAGCACCAAAGTCCTCAGCATG
AAGCTCAACTGAGGAGAGATACCAGTGTACTGGTATATATTAAAAGAAGATTGGCAATGTGTGCAAGAAAGTTAGGAAGA
ATAAGAGAAGCAGTAAAAATAATGAGAGATCTGATGAAAGAATTTCCTCCTCTTACCATGTTGAACATCCATGAAAATCT
CTTAGAATCAATTTTAGAATTACAGGCCTATGCAGATGTTCAGGCAGTCCTAGCAAAGTATGATGATATAAGCCTTCCAA
AATCAGCAGCAATCTGTTATACAGCAGCACTGTTGAAGACAAGGACTGTTTCAGATAAATTCTCTCCAGAAACAGCCTCT
AGAAGAGGGTTAAGCACAGCAGAAATTAATGCTGTGGAAGCAATTCATAGAGCTGTGGAATTTAATCCTCATGTTCCAAA
ATATTTACTGAGATGAAAAGTTTGATTTTGCCTCCAGAACACATTCTGAAACGGGGTGATAGTGAAGCACTTGCCTATGC
TTTCTTTCATCTTCAGCACTGGAAGCGAATACAAGGTGCTCTTAATCTCTTACAGTGCACGTGGGAAGGCACTTTTAGAA
TGATTCCATACCCACTAGAGAAAGGACATCTATTTTACCCATATCCCAGCTGCACAGAGACTGCTGATAGAGAGCTGTTA
CCTAACTTTCATCATGTTTCTGTTTACCCAAAGAAAGAACTTCCTTTTTTCATCCATTTCACAGCGGGATTGTGTTCTTC
TACAGCAATGATAGCCCTTCTCACACACCAGTTTCCTGAAATCATGGGTATTTTTGCTAAAGCTGTAAGTATGATCTCAA
GGACTTGTGTAGAGTATTTG

Alignment

ORF - retro_ocun_1940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.55 %
• Parental protein coverage: 73.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSECKVWRNPLNLFRGAEYRRYTWVTGKEPLTYYDMNLSAQDHQTLFTCDTDILRPSDTVMQKAWRERNP
          .SECKVWRNPLNL.RGAEYRRYTWVTGKEPLTYYDMNLSAQDHQTLFT.DTDILRPSDTVMQKAWRERNP
Retrocopy MSECKVWRNPLNLYRGAEYRRYTWVTGKEPLTYYDMNLSAQDHQTLFTGDTDILRPSDTVMQKAWRERNP

Parental  PARIKAAYQALELNNDCATAYVLLAEEEATTIVDAERLFKQALKAGETIYRRSQQCQHHSPQHEAQLRRD
          PARIKAAYQALELNNDCATAYVLLAEEEATTIVDAERLFKQALKAGETIYRRSQQCQH.SPQHEAQLRRD
Retrocopy PARIKAAYQALELNNDCATAYVLLAEEEATTIVDAERLFKQALKAGETIYRRSQQCQHQSPQHEAQLRRD

Parental  TNVLVYIKRRLAMCARKLGRIREAVKIMRDLMKEFPLLTMLNIHENLLESLLELQAYADVQAVLAKYDDI
          T.VLVYIKRRLAMCARKLGRIREAVKIMRDLMKEFP.LTMLNIHENLLES.LELQAYADVQAVLAKYDDI
Retrocopy TSVLVYIKRRLAMCARKLGRIREAVKIMRDLMKEFPPLTMLNIHENLLESILELQAYADVQAVLAKYDDI

Parental  SLPKSAAICYTAALLKTRTVSDKFSPETASRRGLSTAEINAVEAIHRAVEFNPHVPKYLL-EMKSLILPP
          SLPKSAAICYTAALLKTRTVSDKFSPETASRRGLSTAEINAVEAIHRAVEFNPHVPKYLL.EMKSLILPP
Retrocopy SLPKSAAICYTAALLKTRTVSDKFSPETASRRGLSTAEINAVEAIHRAVEFNPHVPKYLL<EMKSLILPP

Parental  EHILKRGDSEAIAYAFFHLQHWKRIEGALNLLQCTWEGTFRMIPYPLEKGHLFYPYPSCTETADRELLPN
          EHILKRGDSEA.AYAFFHLQHWKRI.GALNLLQCTWEGTFRMIPYPLEKGHLFYPYPSCTETADRELLPN
Retrocopy EHILKRGDSEALAYAFFHLQHWKRIQGALNLLQCTWEGTFRMIPYPLEKGHLFYPYPSCTETADRELLPN

Parental  FHHVSVYPKKELPFFIHFTAGLCSSTAMIALLTHQFPEIMGIFAKAVSMISRTCVEYL
          FHHVSVYPKKELPFFIHFTAGLCSSTAMIALLTHQFPEIMGIFAKAVSMISRTCVEYL
Retrocopy FHHVSVYPKKELPFFIHFTAGLCSSTAMIALLTHQFPEIMGIFAKAVSMISRTCVEYL

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	0.17 RPM	11.15 RPM
SRP017611_kidney	0.10 RPM	11.96 RPM
SRP017611_liver	0.08 RPM	4.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1940 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1940 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000269	1 retrocopy	retro_ocun_1940 ,