RetrogeneDB ID: retro_ocun_191

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:23346057..23347107(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000014000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TAF7L
• Ensembl ID: ENSOCUG00000004497
• Aliases: None
• Description: TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa [Source:HGNC Symbol;Acc:11548]

Sequence

>retro_ocun_191
ATGAGTAAGAGCAAAGATGATGCCCCTCATGAGCTGGAGAGCCAGTTTATCTTGCGCCTGCCTCCAGAATATGCTGCTAC
TGTGAGGAGGGCAGTGCAGTCGGGGCATGTCAACCTGAAAGACAGACTGACCATCGAGTTACACCCCGATGGGCGTCATG
GAATTGTCAGAGTGGACCGGGTCCCTCTGGCCTCAAAACTGGTGGATCTGCCGTGTGTTATGGAAAGCTTGAAAACCATC
GATAAAAAAACCTTTTACAAGACTGCTGATATCTGTCAGATGCTCGTGTCCACAGTTGATGGTGATCTTTATCCCCCTGT
GGAGGAGCCAGTTGCTGCTGCTGACCCCAAAGCAAGCAAGAAAAAGGATAAGGACAAAGAGAAAAAGTTCGTCTGGAACC
ATGGAATTACTCTGCCTCTAAAGAATGTCAGAAAGAGAAGATTCCGGAAGACAGCAAAGAAAAAGTATATTGAGTCTCCA
GACGTGGAGAAAGAAGTGAAGCGGTTGCTGAGTACAGATGCGGAAGCTGTCAGTACTCGCTGGGAGATAATTGCTGAAGA
TGAAACAAAAGAGACGGAGAATCAAGGCCTTGACATCTCTTCCCCAGGAATGTCTGGCCACAGGCAGGGCCAGGACTCCC
TGGAGCACGATGAGCTTCGGGAGATATTCAATGACCTCAGCAGCAGCAGCGAGGATGAAGATGACACCCAGCACCAGGAC
GAAGAAGATATAAACATCATCGACACTGAGGAAGACCTGGAGAGACAGCTGCAGGACAAGCTGAATGAGTCAGATGAACA
GCACCAAGAAAACGAAGGGACCAACCAGCTGGTTATGGGCATTCAGAAGCAGATTGACAACATGAAAGGCAAGCTCCAGG
AGACCCAGGACAGGGCCAAGCGACAGGAGGATCTCATCATGAAGGTGGAAAACCTGGCTCTCAAGAACAGATTTCAGGCT
GTGCTGGATGAGTTAAAACAAAAGGAAGACCGAGAAAAGGAGCAGCTCAGCTCTTTGCAGGAAGAGCTGGAGTCACTCCT
AGAGAAGTAA

Alignment

ORF - retro_ocun_191 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.26 %
• Parental protein coverage: 64.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTKSQDEVPHELENQFILRVPPEYASTIRKMVRSRDVAMKDKLKIDLSPDGRRATVEVDKVSLAAKLVDL
          M.KS.D..PHELE.QFILR.PPEYA.T.R..V.S..V..KD.L.I.L.PDGR...V.VD.V.LA.KLVDL
Retrocopy MSKSKDDAPHELESQFILRLPPEYAATVRRAVQSGHVNLKDRLTIELHPDGRHGIVRVDRVPLASKLVDL

Parental  PCVVGSMKTFDKKTFFTTADISQMLVCTTADDQPQSSPEEPVASADLDLMDISEREKKKSYTWKHGITPP
          PCV..S.KT.DKKTF..TADI.QMLV..T.D.......EEPVA.AD..........K.K...W.HGIT.P
Retrocopy PCVMESLKTIDKKTFYKTADICQMLV-STVDGDLYPPVEEPVAAADPKASKKKDKDKEKKFVWNHGITLP

Parental  LKNVRKKRFRKTTKKRYVDSPAVEKEVKRLLYSDAEAISARWEVIAEGEDKEIESQGCISGFKIS-PGSS
          LKNVRK.RFRKT.KK.Y..SP.VEKEVKRLL..DAEA.S.RWE.IA..ED...E......G..IS.PG.S
Retrocopy LKNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEIIA--EDETKETEN--QGLDISSPGMS

Parental  GEKRGRISSESIEYN-ILREMFSFSIDNE----EEEETSSTTDCEEDLERELQAKLLESN-LYKSKEASN
          G...G..S.E..E...I.....S.S.D........EE.....D.EEDLER.LQ.KL.ES.......E..N
Retrocopy GHRQGQDSLEHDELREIFNDLSSSSEDEDDTQHQDEEDINIIDTEEDLERQLQDKLNESDEQHQENEGTN

Parental  ALVLTIQKQIHFLERKLRNIQCQTQRQNHLFMKVESLPLKNHLKSVLEKLNLEEKQRNEQLISLQEKLKC
          .LV..IQKQI.....KL...Q....RQ..L.MKVE.L.LKN....VL..L...E....EQL.SLQE.L..
Retrocopy QLVMGIQKQIDNMKGKLQETQDRAKRQEDLIMKVENLALKNRFQAVLDELKQKEDREKEQLSSLQEELES

Parental  ILKK
          .L.K
Retrocopy LLEK

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	65.95 RPM	0.11 RPM
SRP017611_kidney	81.59 RPM	0.20 RPM
SRP017611_liver	26.90 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_191 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_191 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_191 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009247	1 retrocopy	retro_amel_6,
Bos taurus	ENSBTAG00000001979	1 retrocopy	retro_btau_107,
Loxodonta africana	ENSLAFG00000006941	1 retrocopy	retro_lafr_209,
Mus musculus	ENSMUSG00000009596	1 retrocopy	retro_mmus_72,
Oryctolagus cuniculus	ENSOCUG00000004497	1 retrocopy	retro_ocun_191 ,
Rattus norvegicus	ENSRNOG00000026315	1 retrocopy	retro_rnor_134,