RetrogeneDB ID: retro_ocun_1429

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:96309458..96310099(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000028152
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000007316
• Aliases: None
• Description: None

Sequence

>retro_ocun_1429
ATCACCCTGAAGGCCTTCCAGCAGCAGCCTTTCAGATCAACACAGAACCCGAGGAGACAGTGAGAGCACTGAAAGAGAAA
ACTCAATCTGAAAAGGGAGAAGATGCCTTTTTGGTAGTGGGACAACAATTAATTTAAGCCAGCAAACTCCTCACTAATGG
CACTGCTCTCAAAGAATATAAAATTGATGAGGAAAGTACTGTGGTGGTAATGGTGACAAAACCCAGAGCAGTGACAGCAC
CATCAACAGCGACAACTCAGCATTCAAATCCTGCCACCATGGCAGTTAGTTCCTCCCCAGCACCCCCTGTAACTCAGGCC
CCAACACCTGCCCTGGCTGTGACTGCCTCTTCTATGCCTGCCTCCATGGTTCCAGCATCAATGACAGCATCTTCTGAACC
TGCACCTGCTAGAGCAACTACGTGAGAGAAACCTGCAGAAAAGCTGGTAGACATGCCAGCGCCTACTGGCCCAGTATCAG
CTGACAGTAAGCCAGGGAACTGTTCCTCGATCAAACCTTCTTGACGATGCAACAAGTACACTTGTGTCAGGCCAGACTTA
CGACAAGATGGTGACTGAGATGTCAATGGGCTATGAATGAGGAAAGTCCTTGTAGCTCTGAGAGCCAGTTTCAACAACCC
T

Alignment

ORF - retro_ocun_1429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.84 %
• Parental protein coverage: 52.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTLKTLQQQTFK-IDIDPEETVKALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFVV
          .TLK..QQQ.F..I...PEETV.ALKEK..SEKG.DAF.V.GQ.LI.A.K.L...TALKEYKIDE...VV
Retrocopy ITLKAFQQQPFR<INTEPEETVRALKEKTQSEKGEDAFLVVGQQLI*ASKLLTNGTALKEYKIDEESTVV

Parental  VMVTKPKAVTTPAPATTQQSNSATTTAVSSSTATAVTQASTPAPALAPTSTPASIAPAS-TTSSEPAPAS
          VMVTKP.AVT.P..ATTQ.SN.A.T.AVSSS.A..VTQA.TPA.A....S.PAS..PAS.T.SSEPAPA.
Retrocopy VMVTKPRAVTAPSTATTQHSNPA-TMAVSSSPAPPVTQAPTPALAVTASSMPASMVPASMTASSEPAPAR

Parental  ATKQEKPAEKPVETPVATSPTSTDSTSGDSS-RSNLFEDATSALVTGQSYENMVTEIMSMGYE-REQVIA
          AT..EKPAEK.V..P..T.P.S.DS..G..S.RSNL..DATS.LV.GQ.Y..MVTE.MSMGYE....V..
Retrocopy ATT*EKPAEKLVDMPAPTGPVSADSKPGNCS>RSNLLDDATSTLVSGQTYDKMVTE-MSMGYE<MRKVLV

Parental  ALRASFNNP
          ALRASFNNP
Retrocopy ALRASFNNP

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	72.46 RPM
SRP017611_kidney	0.00 RPM	88.18 RPM
SRP017611_liver	0.08 RPM	68.75 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1429 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429 ,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,