RetrogeneDB ID: retro_ocun_78

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:62637670..62638654(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000029734
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004329
• Aliases: None
• Description: None

Sequence

>retro_ocun_78
ATGGATAAGAAGAAAGTGTTGGTCAAGGTGCATCCCGAGGGCAAGTTTGTCGTAGACGTGGACAAGAACATCGACATCAA
TGATGTGACGCCCAACTGCCGGGTTGCACTCAGAAACGACAGCTACACTCTGCACAAGATCCTGCCCAACAAAGTGGACC
CCCTCGTGTCACTCATGATGGTGGAGAAGGTGCCAGACTCCACCTACGAAATGATCGGGGGACTGGACAAGCAGATCAAG
GAGATCAAAGAAGTGATCGAGCTGCCTGTCAAGCACCTTGAGTTCTTTGAAGCCCTGGGCATCGCACAATCCAAGGGAGT
GCTGCTGTACGGACCCCCAGGCACCGGGAAGACTTTGTTGGCCCGCGCTGTGGCTCATCACACTGACTGTACCTTTATCC
GCGTCTCCGGCTCTGAACTGGTACAGAAATTCATCGGAGAAGGGGCAAGAATGGTGCGGGAGCTGCTTGTCATGGCACGA
GAACACGCTCCATCCATCATCTTCATGGACGAAATCGACTCCATCGGCTCCTCGCGGCTGGAGGGAGGCTCTGGAGGGGA
CAGCGAAGTGCAGCGCATGATGCTTGAGCTGCTCAACCAGCTGGACGGCTTCGAGGCCACCAAGAACATCAAGGTCATCA
TGGCTACTAATAGGATTGACATCTTGGATTCCACTCTGCTTCGCCCAGGACGCATCGACAGAAAAATTGAATTCCCACCC
CCCAATGAAGAGGCTCGGCTGGACATCTTAAAGATCCATTCTCGGAAAATGAACCTGACCCCGGGGATCAACCTGAGAAA
AATTGCTGAGCTGATGCCAGGAGCGTCAGGGGCTGAAGTTAAGGGTATGTGCACAGAGGCCGGCATGTATGCCCTGCGGG
AATGGCGAGTCCATGTCACCCAGGAGGACTTCGAGATGGCAGTTGCCAAGGTCATGCAAAAGGACAGTGAGAAGAACATG
CCCATTAAGAAACTATGGAAGTGA

Alignment

ORF - retro_ocun_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.94 %
• Parental protein coverage: 80.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYE
          MDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYE
Retrocopy MDKKKVLVKVHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEKVPDSTYE

Parental  MIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSEL
          MIGGLDKQIKEIKEVIELPVKH.E.FEALGIAQ.KGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSEL
Retrocopy MIGGLDKQIKEIKEVIELPVKHLEFFEALGIAQSKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSEL

Parental  VQKFIGEGARMVRELFVMAREHAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRTMLELLNQLDGFEATKNI
          VQKFIGEGARMVREL.VMAREHAPSIIFMDEIDSIGSSRLEGGSGGDSEVQR.MLELLNQLDGFEATKNI
Retrocopy VQKFIGEGARMVRELLVMAREHAPSIIFMDEIDSIGSSRLEGGSGGDSEVQRMMLELLNQLDGFEATKNI

Parental  KVIMATNRIDILDSALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEV
          KVIMATNRIDILDS.LLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLT.GINLRKIAELMPGASGAEV
Retrocopy KVIMATNRIDILDSTLLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTPGINLRKIAELMPGASGAEV

Parental  KGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDSEKNMSIKKLWK
          KG.CTEAGMYALRE.RVHVTQEDFEMAVAKVMQKDSEKNM.IKKLWK
Retrocopy KGMCTEAGMYALREWRVHVTQEDFEMAVAKVMQKDSEKNMPIKKLWK

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	1.32 RPM	10.21 RPM
SRP017611_kidney	0.71 RPM	11.76 RPM
SRP017611_liver	0.92 RPM	5.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_78 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_78 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_78 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78 ,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,