RetrogeneDB ID: retro_ocun_1223

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:19748526..19749426(+)
• Located in intron of: ENSOCUG00000013706

Retrocopy information

• Ensembl ID: ENSOCUG00000028142
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUPT7L
• Ensembl ID: ENSOCUG00000010219
• Aliases: None
• Description: suppressor of Ty 7 (S. cerevisiae)-like [Source:HGNC Symbol;Acc:30632]

Sequence

>retro_ocun_1223
TCCCCTCCTCTCCTTGCTGACCTCCTGCCTTTGGACTGTAAGAACCCCAATGCACCATTCCAGATCCGGCACAGTGACCC
AGAGAGTGACTTTCATCATGGAAAAGAGGAACCTGTGACCGAACTCAGCCAGCATTCCTGTCGGCACCTCCTCTTCTACG
CAGTGGCCACAATCCTGGCCCACACAGTCTTCGAGTGTGCTAATGAAAGTGTCTTGGAGACCCTCACTGATGTGGCGCAT
GAGTGTTGCCTTAAGTTCACCAAGCTGCTGCACTTTGCTAAGAATCAGGAGGCTCAGCTGGAACAGACTCCTTTCCCGGA
TGTTATGGAGCAGGTGTTCCACGAGGTGGGCATTGGCAGTGTGCTCTCTTTCCAGGAGTTCTGGCAGCACCGCATCAAGG
ACTGTCACACTTAATGCTACAGATTAGTAAGCGACTCTCTGAAGAGTATGAAAGGATTGTCAATCCTGAGAAGGCCACTG
AGGACAGCAAACCCATGAAGATCAAGGAGGAGCCTGTGGGTGACATCACCTCTCTCCTCAGTGTAGAATTGGAGGCTGAC
CTGGCTTCTGGGGACCAGTCCCTGCCCATGGGAGTCCTTGGAGCTCAGAGTGAGCACTTCCCATCTAACCTAGAGGGTGA
AACTTTGCCTCAGGCTTCCATTGTGGAGGTAAAGGCTTCTCCTCTTTGGAATCTGGCCCACTTGAAAATGGAGTCTCAAG
AGAGTGAAGAGGGCAGTGTCTGGGGCATGCTGTCCTGGGCAGTGATGTCTACTGGGAACCCATGTCAGGCATGAACGGAG
CCGGATCCCCCAGAGCTCTGATGGCTCAGAGAGCAGCTATGGTTCCCACTCCACTGAGAGCCTCATGGGGTCCTCCCCTG
TTTTCAACCAGCGCTGCAGA

Alignment

ORF - retro_ocun_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.58 %
• Parental protein coverage: 73.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SPPLPDDLLPLDCKNPNAPFQIRHSDPESDFYRGKGEPVTELSWHSCRQLLYQAVATILAHAGFECANES
          SPPL..DLLPLDCKNPNAPFQIRHSDPESDF..GK.EPVTELS.HSCR.LL..AVATILAH..FECANES
Retrocopy SPPLLADLLPLDCKNPNAPFQIRHSDPESDFHHGKEEPVTELSQHSCRHLLFYAVATILAHTVFECANES

Parental  VLETLTDVAHEYCLKFTKLLRFAVDREARLGQTPFPDVMEQVFHEVGIGSVLSLQRFWQHRIKDYHT-YM
          VLETLTDVAHE.CLKFTKLL.FA...EA.L.QTPFPDVMEQVFHEVGIGSVLS.Q.FWQHRIKD.HT..M
Retrocopy VLETLTDVAHECCLKFTKLLHFAKNQEAQLEQTPFPDVMEQVFHEVGIGSVLSFQEFWQHRIKDCHT<LM

Parental  LQISKQLSEEYERIVNPEKATEDTKPVKIKEEPVSDIPFPVSEELEADLAAGDQSLPMGVLGAQSERFPS
          LQISK.LSEEYERIVNPEKATED.KP.KIKEEPV.DI....S.ELEADLA.GDQSLPMGVLGAQSE.FPS
Retrocopy LQISKRLSEEYERIVNPEKATEDSKPMKIKEEPVGDITSLLSVELEADLASGDQSLPMGVLGAQSEHFPS

Parental  NLEVEASPQASSAEVNASPLWNLAHVKMEPQESEEGNV-SGHGVLGSDVFEEPMSGMSEAG-IPQSPDDS
          NLE.E..PQAS..EV.ASPLWNLAH.KME.QESEEG.V..GH.VLGSDV..EPMSGM..AG.IPQS.D.S
Retrocopy NLEGETLPQASIVEVKASPLWNLAHLKMESQESEEGSV<LGHAVLGSDVYWEPMSGMNGAG<IPQSSDGS

Parental  DSSYGSHSTDSLMGSSPVFNQRCK
          .SSYGSHST.SLMGSSPVFNQRC.
Retrocopy ESSYGSHSTESLMGSSPVFNQRCR

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	0.00 RPM	14.46 RPM
SRP017611_kidney	0.00 RPM	6.08 RPM
SRP017611_liver	0.08 RPM	1.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1223 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1223 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	ENSOCUG00000010219	1 retrocopy	retro_ocun_1223 ,