RetrogeneDB ID: retro_ocun_1046

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:69704560..69705157(+)
• Located in intron of: ENSOCUG00000014197

Retrocopy information

• Ensembl ID: ENSOCUG00000024715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TIMM50
• Ensembl ID: ENSOCUG00000002166
• Aliases: None
• Description: translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23656]

Sequence

>retro_ocun_1046
TATCAAAAGACAAAGGCGCCCTGGCTTGCTGGGCTGCTTGGGGCCGGCGGGACCGTGAGCATCGTCTACATCTTCGGAAA
CAACCCTGTGGATGAAAACGGTGCCAAGATTCCTGATGAGTTCGACAATGATCCGATTCTGGTACAGCAGCTGCGCCGGA
CCTACAAATATTTCAAGGACTACAGACAGATGATCATCCAGCCCACCAGCCCCTGCCTCCTGCCAGACCCCCTGCGGGAG
CCCTACTACCAGCCGCCCTACACGCTCGTCCTGGAGCTCACTGGCGTTCTCTTGCACCCTGAGCGGTCGCTGGCCACAGG
CTGGAGGTTTAAGAAGCGCCCAGGCATCGAGACGCTGTTCCAGCAGCTCGCCCCTCTGTATGAAATCGTCATCTTCACGT
CAGAGACCGGCATGACTGCGTTCCCGCTCATCGACAGCGTGGACCCCCACGGCTTCATCTCCTACCGCCTGTTCCGGGAT
GCCACACGATACATGGATGGGCACCACGTGAAGGACATTTCCTGTCTGAATCGGGACCCAGCCCGCGTGGTGCTTGTGGA
CTGCAAGAAGGAAGCCTTCCGCCTACAGCCGTAAAAC

Alignment

ORF - retro_ocun_1046 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.98 %
• Parental protein coverage: 53.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAKKVALWLAGLLGAGGTVSIVYIFGNNPVDENGAKIPDEFDNDPILVQQLRRTYKYFKDYRQMIIEPTS
          Y.K..A.WLAGLLGAGGTVSIVYIFGNNPVDENGAKIPDEFDNDPILVQQLRRTYKYFKDYRQMII.PTS
Retrocopy YQKTKAPWLAGLLGAGGTVSIVYIFGNNPVDENGAKIPDEFDNDPILVQQLRRTYKYFKDYRQMIIQPTS

Parental  PCLLPDPLREPYYQPPYTLVLELTGVLLHPEWSLATGWRFKKRPGIETLFQQLAPLYEIVIFTSETGMTA
          PCLLPDPLREPYYQPPYTLVLELTGVLLHPE.SLATGWRFKKRPGIETLFQQLAPLYEIVIFTSETGMTA
Retrocopy PCLLPDPLREPYYQPPYTLVLELTGVLLHPERSLATGWRFKKRPGIETLFQQLAPLYEIVIFTSETGMTA

Parental  FPLIDSVDPHGFISYRLFRDATRYMDGHHVKDISCLNRDPARVVVVDCKKEAFRLQPYN
          FPLIDSVDPHGFISYRLFRDATRYMDGHHVKDISCLNRDPARVV.VDCKKEAFRLQP.N
Retrocopy FPLIDSVDPHGFISYRLFRDATRYMDGHHVKDISCLNRDPARVVLVDCKKEAFRLQP*N

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	0.28 RPM	40.18 RPM
SRP017611_kidney	0.20 RPM	37.70 RPM
SRP017611_liver	0.15 RPM	14.72 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1046 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1046 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1046 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000019376	1 retrocopy	retro_mmul_143,
Oryctolagus cuniculus	ENSOCUG00000002166	1 retrocopy	retro_ocun_1046 ,
Drosophila melanogaster	FBgn0250874	2 retrocopies	retro_dmel_72, retro_dmel_8,