RetrogeneDB ID: retro_ocun_1862

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019556:1283..2121(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025646
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A5
• Ensembl ID: ENSOCUG00000013268
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5 [Source:HGNC Symbol;Acc:10991]

Sequence

>retro_ocun_1862
GCCATCTCCAAGTCCGCGGTGGCGCCCATCGAGGGGGTCAAGCTGCTGCTGCAGGTGCAGCATGCCAGCAAGCAAATCAC
TGCCGATAAGCAACACAAGGGCATTCTAGACCGCGTGGTTCGTATCCCCACGGAGCAGGGAGTCCTGTCCTTCTGGCGTG
GTAACCTGGCCAATGTCATCAGCTACTTCCCCACCCAGGCTGTCAACTTTGCCTTCAAAGATAAATACAAGCAGATCCTT
CTGGGTGGCGTGGACAAGAGGACCCAGTGTTGGCACTACTTTGCAGGAAATCTGGCATCAGGTGGTGCTGCTGGAGCCAC
ATCCTGTGTTTCGTGTACCCTCTTGATTTTGCCCGTACCCGTCTAGCAGCTGACGTGGGCAAAGCTGGAGCTGAAAGGGG
ATTCAGAGGCCTCGGTGACTGCCTGGTTAAGATCTACAAATCTGGAGGGATTAGGGGCCTGTACCAAGGCTTTAATGTGT
CTGTACAGGGCATTATCATCTACCGGGCTGCCTGCCTCGGTATCTCTGACACCACAGAAGGAACACTTCCAGGTCCCGGA
ACACGCACATCTTCACCAGCTGGGTGATCGCGCAGTCTGTCACTGCTGTTGCTGGGTTGACTTCCTCCTATCCATTCGAC
ACTGTTCGTCGGCGCATGATGACGCAGTCGGGGCGTAAAGGAACTGATGTCATGTACACAGGCACACTTGACTGCTGGAG
GAAGATCACTCGTGATGAAGGAGGCAAAGCGTTTTTCAAGGGTGCATGGTCCAACGTCCCCAGAGGCATGGGTGGTGCTT
TTGTGCTTGTCTTGTATGATGAAATCAAGAAGTTCACG

Alignment

ORF - retro_ocun_1862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 93.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AISKTAVAPIERVKLLLQVQHASKQITADKQYKGIIDCVVRIPKEQGVLSFWRGNLANVIRYFPTQALNF
          AISK.AVAPIE.VKLLLQVQHASKQITADKQ.KGI.D.VVRIP.EQGVLSFWRGNLANVI.YFPTQA.NF
Retrocopy AISKSAVAPIEGVKLLLQVQHASKQITADKQHKGILDRVVRIPTEQGVLSFWRGNLANVISYFPTQAVNF

Parental  AFKDKYKQIFLGGVDKRTQFWRYFAGNLASGGAAGATS-LCFVYPLDFARTRLAADVGKAGAEREFRGLG
          AFKDKYKQI.LGGVDKRTQ.W.YFAGNLASGGAAGATS.LCFVYPLDFARTRLAADVGKAGAER.FRGLG
Retrocopy AFKDKYKQILLGGVDKRTQCWHYFAGNLASGGAAGATS<LCFVYPLDFARTRLAADVGKAGAERGFRGLG

Parental  DCLVKIYKSDGIRGLYQGFNVSVQGIIIYRAAYFGIYDTAKGMLPDP-KNTHIFISWMIAQSVTAVAGLT
          DCLVKIYKS.GIRGLYQGFNVSVQGIIIYRAA..GI.DT..G.LP.P..NTHIF.SW.IAQSVTAVAGLT
Retrocopy DCLVKIYKSGGIRGLYQGFNVSVQGIIIYRAACLGISDTTEGTLPGP<RNTHIFTSWVIAQSVTAVAGLT

Parental  -SYPFDTVRRRMMMQSGRKGTDIMYTGTLDCWRKIARDEGGKAFFKGAWSNVLRGMGGAFVLVLYDEIKK
          .SYPFDTVRRRMM.QSGRKGTD.MYTGTLDCWRKI.RDEGGKAFFKGAWSNV.RGMGGAFVLVLYDEIKK
Retrocopy SSYPFDTVRRRMMTQSGRKGTDVMYTGTLDCWRKITRDEGGKAFFKGAWSNVPRGMGGAFVLVLYDEIKK

Parental  FT
          FT
Retrocopy FT

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	40.62 RPM
SRP017611_kidney	0.00 RPM	231.19 RPM
SRP017611_liver	0.00 RPM	8.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1862 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1862 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000143	1 retrocopy	retro_amel_1291,
Canis familiaris	ENSCAFG00000018384	2 retrocopies	retro_cfam_1473, retro_cfam_1641,
Callithrix jacchus	ENSCJAG00000005125	1 retrocopy	retro_cjac_373,
Dasypus novemcinctus	ENSDNOG00000008384	1 retrocopy	retro_dnov_1894,
Echinops telfairi	ENSETEG00000004900	2 retrocopies	retro_etel_23, retro_etel_48,
Felis catus	ENSFCAG00000007057	2 retrocopies	retro_fcat_1035, retro_fcat_127,
Homo sapiens	ENSG00000005022	7 retrocopies	retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Gorilla gorilla	ENSGGOG00000014279	8 retrocopies	retro_ggor_1673, retro_ggor_1674, retro_ggor_2146, retro_ggor_2377, retro_ggor_2512, retro_ggor_2517, retro_ggor_2840, retro_ggor_941,
Loxodonta africana	ENSLAFG00000029398	1 retrocopy	retro_lafr_844,
Microcebus murinus	ENSMICG00000002757	3 retrocopies	retro_mmur_322, retro_mmur_411, retro_mmur_974,
Myotis lucifugus	ENSMLUG00000015742	4 retrocopies	retro_mluc_139, retro_mluc_1580, retro_mluc_2564, retro_mluc_86,
Macaca mulatta	ENSMMUG00000022663	6 retrocopies	retro_mmul_1022, retro_mmul_1287, retro_mmul_1699, retro_mmul_1775, retro_mmul_1800, retro_mmul_2090,
Nomascus leucogenys	ENSNLEG00000014852	7 retrocopies	retro_nleu_131, retro_nleu_1314, retro_nleu_1383, retro_nleu_1679, retro_nleu_2253, retro_nleu_2560, retro_nleu_3105,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Oryctolagus cuniculus	ENSOCUG00000013268	11 retrocopies	retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862 , retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Otolemur garnettii	ENSOGAG00000010008	7 retrocopies	retro_ogar_1131, retro_ogar_1275, retro_ogar_1669, retro_ogar_2161, retro_ogar_2408, retro_ogar_2450, retro_ogar_2474,
Pongo abelii	ENSPPYG00000020669	5 retrocopies	retro_pabe_1006, retro_pabe_2587, retro_pabe_3130, retro_pabe_3141, retro_pabe_3398,
Pteropus vampyrus	ENSPVAG00000014924	2 retrocopies	retro_pvam_1118, retro_pvam_911,
Rattus norvegicus	ENSRNOG00000039980	11 retrocopies	retro_rnor_1242, retro_rnor_1364, retro_rnor_1475, retro_rnor_1612, retro_rnor_1904, retro_rnor_1922, retro_rnor_2533, retro_rnor_2758, retro_rnor_721, retro_rnor_722, retro_rnor_723,
Ictidomys tridecemlineatus	ENSSTOG00000020438	3 retrocopies	retro_itri_314, retro_itri_532, retro_itri_868,
Tupaia belangeri	ENSTBEG00000006008	4 retrocopies	retro_tbel_1558, retro_tbel_1860, retro_tbel_4654, retro_tbel_4661,