RetrogeneDB ID: retro_ocun_533

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:124146978..124147804(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MTIF3
• Ensembl ID: ENSOCUG00000011721
• Aliases: None
• Description: mitochondrial translational initiation factor 3 [Source:HGNC Symbol;Acc:29788]

Sequence

>retro_ocun_533
CTTCTAAAGTGGTTGACACTGCAAAGCATGAAGTCTGAAAATAATTGCATTAGAAGATGCTTTGGTAAATACCTGATGCA
AAAGATAGACCCAGCACAGTTGTCCTTGATTGCTGCTACCCCAAGACCATCCTACCTCATTCATGCAAAAGCTTTTAGTA
CATTGAAATCACTCAGGATGAGAGAAAAAAGACAAAAAAGAAGAAATTGGTTTTAGTAATGTTGGAAGAAAAATTAAGGA
ATGAACTATTCAGGTGCTTGATGAGAAGGGCAATGATTTGGGAAACATGCACCAAGCAGATGTCATCAGGCTAATGAATG
AGTGAAAACTGAGGCTGGTACAGATGCCCATGCAGAGCACCCCCCTCCCCAAGTACCAGCTCATGACAGGCTTACGGATA
CACGAGGAATCCCTTTAGCTCCACGAAATGGAAAAAGCTCAGCCCAAAGATGGACCAATCCTGACAAAAAAGCTAACTTT
CTCTTCAAAAATCAAGCAATATAATTTGGACACAAAGAATAAACAGATTCAGCACTGGATTGAGAGAAAATGCCAAGTTT
AAATTCCTGTAAAGAAGGGAGGAAATGCAGATGAGCCAGAAAACAAAATGGAGGAGCTATTTAATAAAATACTACAAATA
TTGACTGGAATAGCTACCTTCAGATCCAAGCCACAAGCTGTTAAAGTAGGAAAAGCAGTAATGTGTGCACTTCATCATTT
GAGCAAAAAGGAAGAGAACACATATAGAGAATCTAAAGGGACCGAGAAATGAGACACTTTGCACAAAGAAAGTAGAAGTG
ATAGGGAATCAAGTGATCCACATCAG

Alignment

ORF - retro_ocun_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.18 %
• Parental protein coverage: 90.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLKRLILQTVKSENNCIRRCFGEHLMQKTDPAQLSLIASAPRPSYLPHAKAFSTA-EDTQAERKKTKKN-
          .LK.L.LQ..KSENNCIRRCFG..LMQK.DPAQLSLIA..PRPSYL.HAKAFST..E.TQ.ERKKTKK..
Retrocopy LLKWLTLQSMKSENNCIRRCFGKYLMQKIDPAQLSLIAATPRPSYLIHAKAFSTL<EITQDERKKTKKK<

Parental  ETSFSNVGRKIKERIIHVLDEKGNDLGNMHRAEVIRLMDERDLRLVQRDAHAEP-PEYQLMTGLQIHKER
          E..FSNVGRKIKE..I.VLDEKGNDLGNMH.A.VIRLM.E..LRLVQ......P.P.YQLMTGL.IH.E.
Retrocopy EIGFSNVGRKIKE*TIQVLDEKGNDLGNMHQADVIRLMNE*KLRLVQMPMQSTPLPKYQLMTGLRIHEES

Parental  LRLREMEKAQPKAGPILTKELTFSSNIGQHDLDTKNKQIQQWIEKKYQVQITIKKGKNADEPENKTEELF
          L.L.EMEKAQPK.GPILTK.LTFSS.I.Q..LDTKNKQIQ.WIE.K.QV.I..KKG.NADEPENK.EELF
Retrocopy L*LHEMEKAQPKDGPILTKKLTFSSKIKQYNLDTKNKQIQHWIERKCQV*IPVKKGGNADEPENKMEELF

Parental  NQILQTMPGIATFKSKPQAVKGGKAVMCVLRHLSKKEENTYKESQGTQKRDTLHKESRSEKESNDPHQ
          N.ILQ...GIATF.SKPQAVK.GKAVMC.L.HLSKKEENTY.ES.GT.K.DTLHKESRS..ES.DPHQ
Retrocopy NKILQILTGIATFRSKPQAVKVGKAVMCALHHLSKKEENTYRESKGTEK*DTLHKESRSDRESSDPHQ

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	14.07 RPM
SRP017611_kidney	0.00 RPM	13.68 RPM
SRP017611_liver	0.00 RPM	5.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_533 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_533 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004404	1 retrocopy	retro_chof_466,
Homo sapiens	ENSG00000122033	1 retrocopy	retro_hsap_3284,
Gorilla gorilla	ENSGGOG00000008409	1 retrocopy	retro_ggor_1318,
Nomascus leucogenys	ENSNLEG00000000343	1 retrocopy	retro_nleu_1350,
Oryctolagus cuniculus	ENSOCUG00000011721	1 retrocopy	retro_ocun_533 ,
Pongo abelii	ENSPPYG00000005236	1 retrocopy	retro_pabe_2713,
Pan troglodytes	ENSPTRG00000005732	1 retrocopy	retro_ptro_2221,
Tupaia belangeri	ENSTBEG00000012276	3 retrocopies	retro_tbel_4048, retro_tbel_4602, retro_tbel_760,