RetrogeneDB ID: retro_ocun_37

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:21975921..21977049(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024828
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RNF128
• Ensembl ID: ENSOCUG00000012328
• Aliases: None
• Description: ring finger protein 128, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21153]

Sequence

>retro_ocun_37
ATGACTCTACTCAAGAATGGCACTTGGAGAAACAACACTGCATCTTCCTGGCTTCTGAAGTTCACTTTTCTTTGGCTGTT
TAGTCAGTACTCTTGCACAACAAGTGCTGTTTGGACTGCATACATGAACATATCATTTCATGTTGGGAATCGCATGTTGT
CAGAGTTGGGGGAGACTGGAGTATTTGGAAGGGGCTCTGCTTTGAAGAGAGTGACAGGAGTTATAGTGCCACCAGAGGGA
AAAACCCAAAATGCATGTAATCCTACTACCAGTTTCAGCAGAACAAAGAACTCAGAGACATGGCTAGCACTTATTGAACG
GGGAGGTTGTACTTTCACACAGAAAATCAAGGTGGCGACTGAGAAGGGAGCCAGTGGAGTGATCATCTATAACTTTCCAG
GAACTGGCAATCAGGTTTTCCCCATGACTCATCAGGCATTTGAAGGCATTGTTGTGGTTATGATTGGTAACTTAAAAGGT
ATGGAAATTTTGCATTTAATTCAGAAGGGAGTTCATGTAACAGTCATGGTTGATGTGGGGAGAAAACACATCATCTGGAT
GAATCATTATTTTGTCTCTTTTATGATCGTCACAACTGCTACCTTAGCATATTTCGTTTTTTATCATATTCGAAGACTTT
GGATAGCAAGGATTCAGAATAGGAGATGGCAGCGATTAACAACAGATATCAAGAGAGCATTTGGACAACTTCAACTTCGG
GTATTAAAAGAGGGAGATGAGGAAATAACTCCAAATGGCGATAGCTGCGTAGTTTGCTTTGAACTCTATAAGCCTAATGA
TATAGTTCGTATTCTGACTTGTAAACACTTTTTCCACAAGAATTGCATTGACCCCTGGATTCTAGCCCATGGGACATGCC
CCATGTGCAAGTGTGACATTCTTAAAGCTTTGGGAATTCAAGTGGATATTGAAGATGGAACTGAATCTTTACAAGTCCTG
ATGTCAAGTGAATTGCCTGAAATCCTGTCACCTAGAGAAGAGGAGGCAGATAATGAACCTCCTCCTGCAAGGATATCAGA
TAAAGCAACCCACGTGGAGGAGAACCCGACTTCTCAGAATGATGACCGCCAGGCTGATTTAGTTGTGGAAAACGTTCATC
CTTCAACC

Alignment

ORF - retro_ocun_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.91 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQWIQ
          .WLALI.RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PM.H.....IV..MIGNLKG..IL..IQ
Retrocopy TWLALIERGG-CTFTQKIKVATEKGASGVIIYNFPGTGNQVFPMTHQAFEGIVVVMIGNLKGMEILHLIQ

Parental  SGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
          .G..VT....VG.KH..W.NHY...F..V.....TA...........R.L..AR.Q.R....L..D.K.A
Retrocopy KGVHVTVMVDVGRKHIIWMNHYFVSFMIVT----TATLAYFVFYHIRR-LWIARIQNRRWQRLTTDIKRA

Parental  IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
          .G.LQLR.LK.GD.EI.P.GDSC.VC.ELYKPND.VRILTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
Retrocopy FGQLQLRVLKEGDEEITPNGDSCVVCFELYKPNDIVRILTCKHFFHKNCIDPWILAHGTCPMCKCDILKA

Parental  LGIEVDVEDGSVSLQVPVSNETSHSASPHEEDNRSE
          LGI.VD.EDG..SLQV..S.E.....SP.EE....E
Retrocopy LGIQVDIEDGTESLQVLMSSELPEILSPREEEADNE

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	0.55 RPM	15.45 RPM
SRP017611_kidney	0.10 RPM	62.54 RPM
SRP017611_liver	0.08 RPM	47.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_37 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_37 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_37 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2651
Bos taurus	retro_btau_1358
Sus scrofa	retro_sscr_597

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37 ,
Pelodiscus sinensis	ENSPSIG00000010727	1 retrocopy	retro_psin_49,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,