RetrogeneDB ID: retro_ocun_432

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:23064578..23064984(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000003184
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIAA1143
• Ensembl ID: ENSOCUG00000000929
• Aliases: None
• Description: KIAA1143 [Source:HGNC Symbol;Acc:29198]

Sequence

>retro_ocun_432
AGCTGCCATGAGCAGGTGTCCTGTATGAGGCTGGCTGGGCCAACATTCCTGTCCCTCTTCAAGGAGTGGTCACCTACCAA
GAATGGCCTACCATAGAGACCAAGAGAATTCAGCACCAGTTCCCTGATGAAGATGGTGAGAACAGTGACAAAGAAGATGA
GCATCCCCAAGTGGTGGTTTTAAAGGGAGATCAACTAGCTGAAGAAATCATGAAAATTAAAGCAGAAATAAAGGCTGCCA
AAGCAGATGAAGAACCACCTCCAGCTGATGGGAGAATCATGTATCAAAACCAGTTAAGCATCCCTCAGATGAAAAATATT
CAGGTTTAACAGCAAACTCAAAAAAGAAGACAATTGAAGATGAAATGAATAAGCAAGACTCAGAATTCACAAAAGCAAAT
AAAAAA

Alignment

ORF - retro_ocun_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.71 %
• Parental protein coverage: 89.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKRNQVSYVRPAEPAFLSRFKER-IGYQEGPTVETKRIQPQLPEEDDEHSDKEDEQPQVVVLKKGHLSAE
          S...QVS..R.A.P.FLS.FKE....YQE.PT.ETKRIQ.Q.P.ED.E.SDKEDE.PQVVVLK...L.AE
Retrocopy SCHEQVSCMRLAGPTFLSLFKEW<VTYQEWPTIETKRIQHQFPDEDGENSDKEDEHPQVVVLKGDQL-AE

Parental  EVMKIKAEIKAAKADEEPPPADGKIMYR-KPVKRPSDEKYSGLTASSKKKKTNEDEVNKQDSVKKNSQKQ
          E.MKIKAEIKAAKADEEPPPADG.IMY..KPVK.PSDEKYSGLTA.S.KKKT.EDE.NKQDS......K.
Retrocopy EIMKIKAEIKAAKADEEPPPADGRIMYQ<KPVKHPSDEKYSGLTANS-KKKTIEDEMNKQDSEFTKANKK

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	0.39 RPM	7.06 RPM
SRP017611_kidney	0.20 RPM	4.97 RPM
SRP017611_liver	0.15 RPM	4.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_432 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_432 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014132	1 retrocopy	retro_cfam_2208,
Homo sapiens	ENSG00000163807	2 retrocopies	retro_hsap_1399, retro_hsap_2762,
Nomascus leucogenys	ENSNLEG00000005987	1 retrocopy	retro_nleu_666,
Oryctolagus cuniculus	ENSOCUG00000000929	2 retrocopies	retro_ocun_1601, retro_ocun_432 ,
Pongo abelii	ENSPPYG00000013954	1 retrocopy	retro_pabe_2250,
Pan troglodytes	ENSPTRG00000014824	1 retrocopy	retro_ptro_1869,
Pteropus vampyrus	ENSPVAG00000012438	2 retrocopies	retro_pvam_367, retro_pvam_458,
Sus scrofa	ENSSSCG00000011308	2 retrocopies	retro_sscr_844, retro_sscr_874,
Ictidomys tridecemlineatus	ENSSTOG00000010817	1 retrocopy	retro_itri_307,