RetrogeneDB ID: retro_ocun_1677

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018760:195815..196690(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S1
• Ensembl ID: ENSOCUG00000012023
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa [Source:HGNC Symbol;Acc:3265]

Sequence

>retro_ocun_1677
ATTCCAGGTCTAAGTTGTAGATTTTATCAATACAAATTTCCTGAGATGAAGATGAAGTGATGGTGAGTGTAAGATCCACT
GTTGAAATGAGGGCTTATGTCAGCTTGTTGGAGTACAATAACATTGAAGGCATGATTCCTCTCAGTGAATTATCCAGAAG
GCATATTCATTCTATAAACAAACTCATCTGAATTGGCGGGAAGGAATGGGTGGTTGTCAAAGAAAAAGGATATACTGATT
TGTCCAAAAGAAGAGTTTCTCCAGAGGAGGCAATCAAATGTGAAGACAAATTCACAAAATCTAAAACCATGTATAGCATT
CTTTGTCACGTTGCCGAGGTGTTAGAATACACCAAGGATGAGCAACTGGAGGGCCTGCTCCGGAGAACTGCATGGGTCTC
TGATGACAAGTCCAAGAGACCTGAATACGGAGCCTATGATACGTTTAAACATGCAGTATCAGACCCATCTATTTTAGATA
ATTTAGATTTGAATGATGGTAGACAGGAAGTATCCATTAATAATATTAATGGGCGTTTGATTCCATAGGCTGTGAAAATT
CAGGCAGGTATTAAAGTGGTACTGTTATGATTATGAAGGCATTGATGCTATAAAAGAAGCCCTAAGAGCAGGTTTGAATT
TTTCATGGAAACCATGCCTATCAAAATTAATCTAACAGCTCTTCCTTGATATGTGATGACTACAAAAACCCTAGAGAGAA
CAGAAGGTCTCTCTGTCCTCAATCAAACTATGGTAGTTATGAAAGAGAAGATGGAGAGAAAGAGGGTAGTGTTTAATGTT
CAGATGGAGCCCAAAGTGATCACAGATACAGACAAGACAACTCGCAAGGCAGCCGGAGAGGCTCAAGAGAGAAAA

Alignment

ORF - retro_ocun_1677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.59 %
• Parental protein coverage: 93.97 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPGLSCRFYQHKFPEV-EDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNE
          .PGLSCRFYQ.KFPE..ED.VMV.VRS..EM.AYVSLLEYNNIEGMI.LSELSRR.I.SINKLI.IG..E
Retrocopy IPGLSCRFYQYKFPEM<EDEVMVSVRSTVEMRAYVSLLEYNNIEGMIPLSELSRRHIHSINKLI*IGGKE

Parental  CVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFD
          .VVV....KEKGY.DLSKRRVSPEEAIKCEDKFTKSKT.YSIL.HVAEVLEYTKDEQLE.L..RTAWV.D
Retrocopy WVVV----KEKGYTDLSKRRVSPEEAIKCEDKFTKSKTMYSILCHVAEVLEYTKDEQLEGLLRRTAWVSD

Parental  DKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVA-CYGYEGIDAV
          DK.KRP.YGAYD.FKHAVSDPSILD.LDLN....EV.INNIN.RL.P.AVKI.A.I.V..CY.YEGIDA.
Retrocopy DKSKRPEYGAYDTFKHAVSDPSILDNLDLNDGRQEVSINNINGRLIP*AVKIQAGIKVV>CYDYEGIDAI

Parental  KEALRAGLNCS-TETMPIKINLIAPPRYVMTTTTLERTEGLSVLNQAMAVIKEKIEEKRGVFNVQMEPKV
          KEALRAGLN.S..ETMPIKINL.A.P.YVMTT.TLERTEGLSVLNQ.M.V.KEK.E.KR.VFNVQMEPKV
Retrocopy KEALRAGLNFS<METMPIKINLTALP*YVMTTKTLERTEGLSVLNQTMVVMKEKMERKRVVFNVQMEPKV

Parental  VTDTDETELARQLERLERE
          .TDTD.T......E..ER.
Retrocopy ITDTDKTTRKAAGEAQERK

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	35.76 RPM
SRP017611_kidney	0.00 RPM	34.46 RPM
SRP017611_liver	0.00 RPM	13.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1677 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1677 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016311	1 retrocopy	retro_btau_1191,
Callithrix jacchus	ENSCJAG00000015368	1 retrocopy	retro_cjac_2067,
Cavia porcellus	ENSCPOG00000003313	1 retrocopy	retro_cpor_1146,
Echinops telfairi	ENSETEG00000019003	1 retrocopy	retro_etel_279,
Monodelphis domestica	ENSMODG00000009911	1 retrocopy	retro_mdom_1754,
Mus musculus	ENSMUSG00000021116	4 retrocopies	retro_mmus_1342, retro_mmus_1927, retro_mmus_1960, retro_mmus_728,
Oryctolagus cuniculus	ENSOCUG00000012023	1 retrocopy	retro_ocun_1677 ,
Rattus norvegicus	ENSRNOG00000009432	3 retrocopies	retro_rnor_1234, retro_rnor_1423, retro_rnor_2218,
Sarcophilus harrisii	ENSSHAG00000009815	1 retrocopy	retro_shar_560,