RetrogeneDB ID: retro_ocun_264

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:54068407..54069583(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000002546
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PDHA1
• Ensembl ID: ENSOCUG00000014748
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) alpha 1 [Source:HGNC Symbol;Acc:8806]

Sequence

>retro_ocun_264
ATGAGGGAGATGCTGGCTGCCTTTGTCTCCCGTGTGCTGTGGGGGGTGGCCAAGAAGCCAGCTCGCAGAGTGCTGGTGGC
ATCCTGTAACTATTCAAATGATGCCATGTTTGAAATTAAGAAATGTGATCTTTATTTGTTGGACGAGGGTCCTCCGCTGA
CTGCAGTGCTCACGAGAGAAGACGGGCTCAGATACTACAAGATGATGCAGGTTGTTCGGCGCATGGAATTGAAAGCCGAT
CAGTTGTATAAACAGAAATTTATTCGTGGTTTCTGCCATTTGTGTGATGGGCAGGAAGCTTGCTGTGTGGGGCTTGAGGC
AGGTATAAACCCCTCGGATCACGTCATCACATCCTATCGGGCGCATGGCGTGTGCTACACTCGTGGACTCCCTGTCCGGT
CAATCCTTGCAGAGCTGACAGGCAGAAGAGGAGGCTGTGCTAAAGGCAAGGGAGGATCGATGCATATGTATGCCAAGAAC
TTCTATGGGGGCAATGGCATTGTGGGTGCCCAAGTACCCCTGGGAGCTGGTGTCGCTCTGGCCTGTAAGTACATGGGAAA
CAACGAGATCTGCCTGACTTTATATGGGGATGGCGCAGCTAATCAGGGTCAGATAGCCGAAGCTTACAATATGGCAGCTT
TATGGAAACTACCTTGTATTTTCATCTGTGAGAATAACCTCTATGGAATGGGGACATCGGTTGAGAGAGCAGCAGCCAGC
ACTGACTATTACAAGAGAGGCCATTTTATCCCTGGGCTAAGAGTGGATGGAATGGATATTCTGTGTGTTCGGGAGGCAAC
GAGGTTTGCAGCCAACTATTGTAGATCTGGAAAGGGGCCCATACTGATGGAGCTGCAGACCTACCGTTATCATGGACACA
GTATGAGTGATCCTGGCATCAGTTACCGTAGCCGAGAAGAAATTCAAAAAGTAAGAAGCAAGAGTGATCCTATTATGCTT
CTCCAAGATAGGATGGTGAACAGCAAGCTTGCCAGTGTGGAAGAATTAAAGGAAATCGACTCTGAAGTGAGGAAAGAAAT
CGAGGATGCAGCCCAGTTTGCTACAACTGATCCTGAACCCCCTGTAGAAGAATTGGGCCATCACCTCTACAGCAGTAATC
CACCTTTTGAAGTTCGTGGTGCAAATCAGTGGATCAAGTTTAAGTCTGTTAGTTAA

Alignment

ORF - retro_ocun_264 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRKMLAA-VSRVLSGAAQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQ
          MR.MLAA.VSRVL.G.A.KPA.RVLVAS.N..NDA.FEIKKCDL..L.EGPP.T.VLTREDGL.YY.MMQ
Retrocopy MREMLAAFVSRVLWGVAKKPARRVLVASCNYSNDAMFEIKKCDLYLLDEGPPLTAVLTREDGLRYYKMMQ

Parental  TVRRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELT
          .VRRMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGINP.DH.IT.YRAHG...TRGL.VR.ILAELT
Retrocopy VVRRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGINPSDHVITSYRAHGVCYTRGLPVRSILAELT

Parental  GRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYN
          GRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAG.ALACKY.G..E.CLTLYGDGAANQGQI.EAYN
Retrocopy GRRGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGVALACKYMGNNEICLTLYGDGAANQGQIAEAYN

Parental  MAALWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGP
          MAALWKLPCIFICENN.YGMGTSVERAAASTDYYKRG.FIPGLRVDGMDILCVREATRFAA.YCRSGKGP
Retrocopy MAALWKLPCIFICENNLYGMGTSVERAAASTDYYKRGHFIPGLRVDGMDILCVREATRFAANYCRSGKGP

Parental  ILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDA
          ILMELQTYRYHGHSMSDPG.SYR.REEIQ.VRSKSDPIMLL.DRMVNS.LASVEELKEID.EVRKEIEDA
Retrocopy ILMELQTYRYHGHSMSDPGISYRSREEIQKVRSKSDPIMLLQDRMVNSKLASVEELKEIDSEVRKEIEDA

Parental  AQFATADPEPPLEELGHHIYSSNPPFEVRGANQWIKFKSVS
          AQFAT.DPEPP.EELGHH.YSSNPPFEVRGANQWIKFKSVS
Retrocopy AQFATTDPEPPVEELGHHLYSSNPPFEVRGANQWIKFKSVS

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	60.98 RPM
SRP017611_kidney	0.00 RPM	65.58 RPM
SRP017611_liver	0.00 RPM	23.12 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_264 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_264 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_41
Pan troglodytes	retro_ptro_79
Gorilla gorilla	retro_ggor_59
Pongo abelii	retro_pabe_129
Macaca mulatta	retro_mmul_123
Callithrix jacchus	retro_cjac_27
Mus musculus	retro_mmus_63
Bos taurus	retro_btau_100
Equus caballus	retro_ecab_21

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016730	1 retrocopy	retro_amel_400,
Bos taurus	ENSBTAG00000019852	2 retrocopies	retro_btau_100, retro_btau_1807,
Callithrix jacchus	ENSCJAG00000005496	2 retrocopies	retro_cjac_2414, retro_cjac_27,
Dipodomys ordii	ENSDORG00000011848	1 retrocopy	retro_dord_35,
Equus caballus	ENSECAG00000001964	1 retrocopy	retro_ecab_21,
Erinaceus europaeus	ENSEEUG00000005485	1 retrocopy	retro_eeur_580,
Homo sapiens	ENSG00000131828	1 retrocopy	retro_hsap_41,
Gorilla gorilla	ENSGGOG00000013574	1 retrocopy	retro_ggor_59,
Myotis lucifugus	ENSMLUG00000012932	2 retrocopies	retro_mluc_2363, retro_mluc_323,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Mustela putorius furo	ENSMPUG00000003269	1 retrocopy	retro_mputfur_812,
Mus musculus	ENSMUSG00000031299	2 retrocopies	retro_mmus_63, retro_mmus_631,
Nomascus leucogenys	ENSNLEG00000009805	1 retrocopy	retro_nleu_74,
Oryctolagus cuniculus	ENSOCUG00000014748	1 retrocopy	retro_ocun_264 ,
Pongo abelii	ENSPPYG00000020171	1 retrocopy	retro_pabe_129,
Pan troglodytes	ENSPTRG00000021717	1 retrocopy	retro_ptro_79,
Pteropus vampyrus	ENSPVAG00000005420	1 retrocopy	retro_pvam_1306,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,
Sus scrofa	ENSSSCG00000023643	2 retrocopies	retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus	ENSSTOG00000015433	1 retrocopy	retro_itri_1529,
Tupaia belangeri	ENSTBEG00000014313	1 retrocopy	retro_tbel_3327,
Tursiops truncatus	ENSTTRG00000000660	1 retrocopy	retro_ttru_1427,