RetrogeneDB ID: retro_ocun_1495

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:7770940..7771375(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000009170
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TOMM20
• Ensembl ID: ENSOCUG00000021470
• Aliases: None
• Description: translocase of outer mitochondrial membrane 20 homolog (yeast) [Source:HGNC Symbol;Acc:20947]

Sequence

>retro_ocun_1495
ATGGTGGGCCGGAACAGCGCCATCGCCGCCGGCGTATGCGGGGCCCTTTTCATCGGGTATTGCATTTACTTCGACCGCAA
GAGACGGAGTGACCCCAACTTCAAGAACAGGTTGCGAGAACGAAGAAAGAAACAAAAGCTTGCCAAAGAGAGAGCTGGGC
TTTCCAAGTTACCTGACCTTAAAGATGCAGAAGCTGTTCAGAAGTTCTTCCTTGAAGAAATACAGCTTGGTGAAGAGTTA
CTAGCTCAAGGTGAATATGAGAAGGGTGTGGACCATCTGACAAATGCAATTGCTGTATGTGGGCAGCCACAGCAATTGCT
GCAAGTATTGCAGCAAACTCTTCCACTGCCAGTGTTCCAGATGCTGCGCACTAAACTCCCAACAATTAGTCAGAGAATTG
TAAGTGCTCAGAGCTTGGCTGAAGATGATGTGGAA

Alignment

ORF - retro_ocun_1495 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF
          MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF
Retrocopy MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF

Parental  LEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLA
          LEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLP.PVFQML.TKLPTISQRIVSAQSLA
Retrocopy LEEIQLGEELLAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPLPVFQMLRTKLPTISQRIVSAQSLA

Parental  EDDVE
          EDDVE
Retrocopy EDDVE

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	0.22 RPM	51.71 RPM
SRP017611_kidney	1.82 RPM	37.70 RPM
SRP017611_liver	0.15 RPM	13.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1495 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1495 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1495 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000562	5 retrocopies	retro_btau_1025, retro_btau_1147, retro_btau_1357, retro_btau_492, retro_btau_533,
Erinaceus europaeus	ENSEEUG00000000221	1 retrocopy	retro_eeur_544,
Myotis lucifugus	ENSMLUG00000016218	1 retrocopy	retro_mluc_644,
Macaca mulatta	ENSMMUG00000007136	2 retrocopies	retro_mmul_1255, retro_mmul_273,
Monodelphis domestica	ENSMODG00000008452	6 retrocopies	retro_mdom_1112, retro_mdom_1172, retro_mdom_1297, retro_mdom_1527, retro_mdom_1568, retro_mdom_838,
Mus musculus	ENSMUSG00000093904	12 retrocopies	retro_mmus_1437, retro_mmus_1669, retro_mmus_1698, retro_mmus_1990, retro_mmus_2026, retro_mmus_2141, retro_mmus_3142, retro_mmus_3311, retro_mmus_3637, retro_mmus_3655, retro_mmus_457, retro_mmus_935,
Oryctolagus cuniculus	ENSOCUG00000021470	2 retrocopies	retro_ocun_1495 , retro_ocun_795,
Otolemur garnettii	ENSOGAG00000032693	2 retrocopies	retro_ogar_3167, retro_ogar_507,
Pteropus vampyrus	ENSPVAG00000015157	1 retrocopy	retro_pvam_346,
Rattus norvegicus	ENSRNOG00000019980	4 retrocopies	retro_rnor_1191, retro_rnor_1958, retro_rnor_1983, retro_rnor_2103,
Sarcophilus harrisii	ENSSHAG00000015876	3 retrocopies	retro_shar_272, retro_shar_512, retro_shar_669,
Ictidomys tridecemlineatus	ENSSTOG00000027564	3 retrocopies	retro_itri_248, retro_itri_71, retro_itri_820,
Tupaia belangeri	ENSTBEG00000003827	26 retrocopies	retro_tbel_1483, retro_tbel_2215, retro_tbel_2239, retro_tbel_2240, retro_tbel_2340, retro_tbel_2348, retro_tbel_2440, retro_tbel_2472, retro_tbel_2548, retro_tbel_2610, retro_tbel_2619, retro_tbel_3000, retro_tbel_3182, retro_tbel_3204, retro_tbel_3674, retro_tbel_3687, retro_tbel_3729, retro_tbel_3808, retro_tbel_3895, retro_tbel_3949, retro_tbel_4068, retro_tbel_4096, retro_tbel_4136, retro_tbel_4596, retro_tbel_4625, retro_tbel_600,
Tursiops truncatus	ENSTTRG00000002200	4 retrocopies	retro_ttru_1114, retro_ttru_183, retro_ttru_870, retro_ttru_982,
Vicugna pacos	ENSVPAG00000003980	1 retrocopy	retro_vpac_252,