RetrogeneDB ID: retro_ocun_45

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:60585337..60587380(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000006712
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KBTBD6
• Ensembl ID: ENSOCUG00000005273
• Aliases: None
• Description: kelch repeat and BTB (POZ) domain containing 6 [Source:HGNC Symbol;Acc:25340]

Sequence

>retro_ocun_45
ATGCAGTCTCGGGAAGACGCTCCGCGTCCTCACTGCCTCGCCAGTGCCCGCGGTGGGCGGCGGCCCGCGACGACTTCCAA
AGCCTCGGTTTCAGCCTTTTTCACGGGGCCAGAGGAGTTACAGGACTCGGCCCATTCTGCAGCCCTGCTGGCACAGCTCA
AGTCGTTCTATGACGCGCGGCTGCTGTGCGATGTGACCATCGAGGTGGTGTCGCCCGGCTGCGGGCCTGGCACCGGGCGC
CTGTTCCCCTGCAACCGCAACGTGCTGGCCGCCGCGTGCCCCTACTTCCGGAGCATGTTCACGGGCGGCATGCACGAGAG
CCAGCAGGCCCGCGTGACCCTGCACGACGTGGACGCCGCATCCTTCGAGGCCCTGGTGGAGTACTGCTACACGGGCCGTG
TGTCCCTGAGCGAGGCCAACGTGCAGCGCCTCTACACCGCCTCCGACATGCTGCAGCTCGAGTACGTGCGGGAAGCCTGC
GCCTCCTTCCTGGCCCGCCGTCTCGATCTGGCCAACTGCACGGCCATCCTCAAGTTTGCTGATGCCTTTGGCCACCCCAG
TCTGAGATCTCAGGCCCAGGCCTACATAGCTCGCAACTTCAAGCAGCTCAGCGGGATGAGTTCGGTTCGGGAGGAGTCTC
TGGCCGACCTGACGCTGGCCCAGCTGCTGGCCATCCTGCGCCTGGACAGTCTGGACGTAGCGAGTGAGCTGACGGTGTGC
CACGTGGCCCTGCAGTGGCTGGAAGCCGCCCCGGAAGAGCGGGGTCCCAGCGCTGCCGAGGTCTTCAGGTGTATCCGCTG
GTCGCTCTTCACCGAAGGCGATTGGAGCTACCTGGAAGGGCTGCTGACCAAGCCCATCGTGAGGAAGTACTGCCTGGACG
TTATTGAAGGGGCCCGGCGGATGCGCTGTGGTAACATGTTGTGCAAGGCACTGGGGCCCGTGCCAGACAGCGGCACCAGC
AGCAGGAGCAGCAGCTCGCTTGTATCCGCAGGAGAAAATCCACCCCAGAGGCTGGGTATGTGTGCCAAGGAGATGGTGGT
CTTCTTTGGACATCCCCGAAATCCCTTTCTCTGCTACGACCCATACTCGGGGGACATGTATACAATGCCTTCGCCGTTAA
CCACCGTGGCTCGCACTAAGACCATAACCTCCTCTGCTGTCTGCGTCTCTCCAGACCATGACATCTATCTAGCTGCCCAG
CCCAGGAAAGACCTCTGGGTGTACAAACCAGCCCAAAATAGCTGGCAGCAACTCGCAGACTGCTTGCTGTGTCGCGAAGG
CATGGATGTGGCCTATCTCAATGGCTACATTTACATTTTGGGTGGCCGAGACCCAGTGACCGGAGTTAAGCTGAAGGAAG
TGGAATGCTACAGTGTTCAGAGGAACCAGTGGGCACTAGTGGCTCCTGTGCCCCATTCCTTCTATTCCTTTGAACTCCTA
GTGGTCCAGAACTATCTTTATGCTGTCAACAATAAGCGCATGCTCTGCTATGACCCTAGCCACAATCTGTGGCTGAGCTG
CGCTTCTCTTAATTGCAGCGACTTTCAGGAAGCGTGTGTCTTCAACGATGAGATCTATTGTATCTGTGACATACCAGTTA
TGAAGGTCTACAACCCAGCTAGGGGAGAGTGGAGGCGGATTCAGAATATTCCCTTGGACTCAGAGGTCCACAACTACCAG
ATTGTCAATCATGACCGAAAGTTGCTGCTGGTGACGTCCACCAGCCCTCAATGGATAAAGAACCGGGTGACTGTGTATGA
ATACGACACAAGGGGAGACCAGTGGGTTACCGTAGGCGCCATGTTAGGTCTTCTGCAGTTTGAGTCCGGCTTTATTTGCC
TCTGTGCTCGTGTTTATCCCTCTTGCCTTGTACCTGGTCAGAGCTTCATCACTGAGGACGACGATGCTCAAAGTGAGTCT
AGCACGGAATGGGACTTAGATGTGTTGAGTGAGCCAGACTCAGAGTCAGGAAGTTCAAGTTCTTTTTCTGATGCTGAAGT
GTGGGTGCAGGTGGCACCTCAGCGGAGTGCCCAGGACCAGCAG

Alignment

ORF - retro_ocun_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.72 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQSREDAPRSRGLASP-GGRGPEKFEKRTVSAFLRGPQELQDSAHSAAPLAQLRSFCDSRLLCDVTTEVV
          MQSREDAPR...LAS..GGR.P....K..VSAF..GP.ELQDSAHSAA.LAQL.SF.D.RLLCDVT.EVV
Retrocopy MQSREDAPRPHCLASARGGRRPATTSKASVSAFFTGPEELQDSAHSAALLAQLKSFYDARLLCDVTIEVV

Parental  SPGCGPGSGRLFPCNRNMLATSCPYFQSMFTGGTCESQQASVTMHGVDAESFEALLEYCYTGCVSLSEAN
          SPGCGPG.GRLFPCNRN.LA..CPYF.SMFTGG..ESQQA.VT.H.VDA.SFEAL.EYCYTG.VSLSEAN
Retrocopy SPGCGPGTGRLFPCNRNVLAAACPYFRSMFTGGMHESQQARVTLHDVDAASFEALVEYCYTGRVSLSEAN

Parental  AQGLFASSDVLQLEYVREASASFLAS-LDLANCTAIFKFANTFGHAKLRSQAQSFIAHDFKQLSRMGSVP
          .Q.L...SD.LQLEYVREA.ASFLA..LDLANCTAI.KFA..FGH..LRSQAQ..IA..FKQLS.M.SV.
Retrocopy VQRLYTASDMLQLEYVREACASFLARRLDLANCTAILKFADAFGHPSLRSQAQAYIARNFKQLSGMSSVR

Parental  EET-ADRTLAQLLAILGLDSLNTESEQVVGHVALKWIEAGPKERGPSAVEVFKCVRWTLFTKDEQDYLEG
          EE..AD.TLAQLLAIL.LDSL...SE..V.HVAL.W.EA.P.ERGPSA.EVF.C.RW.LFT.....YLEG
Retrocopy EESLADLTLAQLLAILRLDSLDVASELTVCHVALQWLEAAPEERGPSAAEVFRCIRWSLFTEGDWSYLEG

Parental  LLAKPTVKKYCLDVIVKALWMRYGDMQM-SLVPMPDS--TSNASSSVVSAGENPLQRLGVCAKEMVILFG
          LL.KP.V.KYCLDVI..A..MR.G.M....L.P.PDS...S..SSS.VSAGENP.QRLG.CAKEMV..FG
Retrocopy LLTKPIVRKYCLDVIEGARRMRCGNMLCKALGPVPDSGTSSRSSSSLVSAGENPPQRLGMCAKEMVVFFG

Parental  RPKDPFICC-PYSGDIYKVPSPLTCLALTGAVVTFTVCISPDHDIYLAAQSRKELWVYTPAQNSWQQLPD
          .P..PF.C..PYSGD.Y..PSPLT..A.T.......VC.SPDHDIYLAAQ.RK.LWVY.PAQNSWQQL.D
Retrocopy HPRNPFLCYDPYSGDMYTMPSPLTTVARTKTITSSAVCVSPDHDIYLAAQPRKDLWVYKPAQNSWQQLAD

Parental  HLLCHEGMTITYLRGYIYILGGRDPITGVKLKKVECYSVQ--QWVLVASLPHSFMSFDLIISRN-LYTLN
          .LLC.EGM...YL.GYIYILGGRDP.TGVKLK.VECYSVQ..QW.LVA..PHSF.SF.L....N.LY..N
Retrocopy CLLCREGMDVAYLNGYIYILGGRDPVTGVKLKEVECYSVQRNQWALVAPVPHSFYSFELLVVQNYLYAVN

Parental  SKRMYHYDPSHNVRLKCLSVKRSNFHEACVFNDEIYCICDLPVMKIYNPFRAHWRQINNIPMVAETNNHR
          .KRM..YDPSHN..L.C.S...S.F.EACVFNDEIYCICD.PVMK.YNP.R..WR.I.NIP...E..N..
Retrocopy NKRMLCYDPSHNLWLSCASLNCSDFQEACVFNDEIYCICDIPVMKVYNPARGEWRRIQNIPLDSEVHNYQ

Parental  IISHGQKLLLITSRNSGWKKNQVTVYEYDTTEDRWINIGTPLGLLQFDSYFFCLSAQVYPCCLEPGQSFL
          I..H..KLLL.TS....W.KN.VTVYEYDT..D.W...G..LGLLQF.S.F.CL.A.VYP.CL.PGQSF.
Retrocopy IVNHDRKLLLVTSTSPQWIKNRVTVYEYDTRGDQWVTVGAMLGLLQFESGFICLCARVYPSCLVPGQSFI

Parental  TEEDDIPSESSTEWDSGGFNELGSEPSSSSSMADEDLWQELSPVVKAKD
          TE.DD..SESSTEWD.....E..SE..SSSS..D...W....P...A.D
Retrocopy TEDDDAQSESSTEWDLDVLSEPDSESGSSSSFSDAEVWVQVAPQRSAQD

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	0.06 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_45 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_45 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_45 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000005273	1 retrocopy	retro_ocun_45 ,