RetrogeneDB ID: retro_ocun_319

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:159499654..159500799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSOCUG00000015904
• Aliases: None
• Description: transketolase [Source:HGNC Symbol;Acc:11834]

Sequence

>retro_ocun_319
GGCCACCCCACACCATGCTGCAGTGTCAATGGCATTGTGGCTACTATCTTGTTCTACACCATGTGCCACAAAGGCCCTGA
ATACACGGAGCCCTCACAACCACCTCTTAGTGCTCTCCAAGGGTCAAGAAGCTCACATCCTGTAGGAAATCCAGGCTGAA
GTTGGCTTCTTGCCTGAAACAGAACTGCTGAACTTGAGGAAGATCAGTCTGAATTGAACAAGTACTCTATTCTGAACCAG
GGTTTCGTGATGTGGCCACTGGTCCCCTGTGCTCAGACCTTGGGCCTGCCTGTGGCATGGCCTACACAGGCAAATGCTTC
AACAAAACCAGCTACTGAGTCTATGCATGCTGGGGACAGGGAACTGTCCAAGGGTTCCAGGGTTCCAGGTGAGATCATGG
CATGCATCAGCTTCTACAAGCTGGACGACCTTGATGCCATCAATGACCGGGGCCAGAGTGAAGCAGCCCCACAGCAGTAG
CAGGAGGATGTCTATCGGAAATGCTGGGTGGCTTTTGCTGGCACATCACCATTGTGGGTGGATGAAGCACAGAGGAGCTG
TGCAAGGCTTAGACCGGACCAAGAATCAGCCAGCAGCCACCATTCCCAAATCTTCAAGGGCTGAGGGATTTCAGGGATGT
AAGATAAGGAGTCTTGATGGAGAGCCCCTCTCCAGAAATTTGTTGGATCAGATCATTCAGGAAATCTACAGCCAGATCCA
CATGAAAAGGTTTTGGTGACTCCTCCAAGGGATGATGCCCCCTTGGTGGACATGGCCAATATCAACATCCCCACCCTGCC
CAACTACAAAGTTAGAGACAAGATAACTACCTGCAAGGCCTATGCACAGGTCCATAGCTGAGCTGGGCCTTGCCAGGGAC
CATATCATCACCCTGAATTGGGGCACTGAGAAGTCTACCTTCTTGGAGACCTTCAAAAAGGAGTGCCTAGGTCACTTCAT
TGAGGATTTCATTGCAAGCCTAACATGGTGAGCGTTGCCACAGACTGCGCCACATGCAACAGCATAGTGCCCTCCTCAGC
ACTCCTGTGGCCTTCCTCATTTGTACCTCAGACCACATATACAAGGCAGCCATCTCTGAGAGCAACGTCATCAACCTCTG
TGGCTCCCACTGCTGTGTGACCATC

Alignment

ORF - retro_ocun_319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.75 %
• Parental protein coverage: 61.96 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  GHPTSCCSAAEIMAVLFFHTMRYK-AQDPRNPHNDRFILSKGHAAPILYAVWAEAGYLPEAELLNLRKIS
          GHPT.CCS...I.A...F.TM..K.A...R.PHN....LSKG..A.IL....AE.G.LPE.ELLNLRKIS
Retrocopy GHPTPCCSVNGIVATILFYTMCHK>ALNTRSPHNHLLVLSKGQEAHIL*EIQAEVGFLPETELLNLRKIS

Parental  -SDLDGHPVPKQAFT-DVATGSLGQGLGAACGMAYTGKYFDKASYRVY-CLLGDG-ELSEGS--VWEAMA
          .S.L.......Q.F..DVATG.L...LG.ACGMAYTGK.F.K.SY.VY.C.LG.G.ELS.GS....E.MA
Retrocopy <SELNKYSILNQGFV<DVATGPLCSDLGPACGMAYTGKCFNKTSY*VY<CMLGTG<ELSKGSRVPGEIMA

Parental  FASFYKLDNLVAILDVNRLGQSDPAPLQHQLDVYQKRCEAFG-WHTIIVDGHSVEELCKA-FGQAKHQPT
          ..SFYKLD.L.AI...N..GQS..AP.Q.Q.DVY.K...AF..WH..IV.G.S.EELCKA.....K.QP.
Retrocopy CISFYKLDDLDAI---NDRGQSEAAPQQ*QEDVYRKCWVAFA<WHITIVGG*STEELCKA<LDRTKNQPA

Parental  AIIAKTFKGRGITGIEDKESWHGKPLPKNMADQVIQEIYSQIQSK-KKILATPPQEDAPSVDISNIRMPT
          A.I.K.....G..G.....S..G.PL..N..DQ.IQEIYSQI..K.K.....P...DAP.VD..NI..PT
Retrocopy ATIPKSSRAEGFQGCKIR-SLDGEPLSRNLLDQIIQEIYSQIHMK<KVLVTPP-RDDAPLVDMANINIPT

Parental  PPSYKVGDKIATRKAYGQ-ALAKLGHASDRIIALDGDTKNSTFSDLFKKEHPDRFIECYIA-EQNMVSVA
          .P.YKV.DKI.T.KAY.Q...A.LG.A.D.II.L...T..STF...FKKE....FIE..IA...NMVSVA
Retrocopy LPNYKVRDKITTCKAYAQ>SIAELGLARDHIITLNWGTEKSTFLETFKKECLGHFIEDFIA<KPNMVSVA

Parental  VGCATRNRTVP-FCSSFAAFFTRAFDQIRMAAISESN-INVCGSHCGVSI
          ..CAT.N..VP...S...AF.....D.I..AAISESN.IN.CGSHC.V.I
Retrocopy TDCATCNSIVP<LLSTPVAFLICTSDHIYKAAISESNVINLCGSHCCVTI

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	107.89 RPM
SRP017611_kidney	0.00 RPM	100.14 RPM
SRP017611_liver	0.00 RPM	104.21 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_319 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_319 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003758	1 retrocopy	retro_btau_176,
Callithrix jacchus	ENSCJAG00000007253	1 retrocopy	retro_cjac_2128,
Cavia porcellus	ENSCPOG00000000072	1 retrocopy	retro_cpor_45,
Dipodomys ordii	ENSDORG00000001392	1 retrocopy	retro_dord_329,
Homo sapiens	ENSG00000163931	1 retrocopy	retro_hsap_47,
Macropus eugenii	ENSMEUG00000005312	3 retrocopies	retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus	ENSMLUG00000000943	1 retrocopy	retro_mluc_67,
Macaca mulatta	ENSMMUG00000014433	1 retrocopy	retro_mmul_74,
Mus musculus	ENSMUSG00000021957	1 retrocopy	retro_mmus_220,
Oryctolagus cuniculus	ENSOCUG00000015904	2 retrocopies	retro_ocun_319 , retro_ocun_62,
Otolemur garnettii	ENSOGAG00000016911	1 retrocopy	retro_ogar_5,
Ochotona princeps	ENSOPRG00000009891	1 retrocopy	retro_opri_10,
Pan troglodytes	ENSPTRG00000015024	1 retrocopy	retro_ptro_126,
Pteropus vampyrus	ENSPVAG00000016283	1 retrocopy	retro_pvam_352,
Rattus norvegicus	ENSRNOG00000016064	1 retrocopy	retro_rnor_146,
Sarcophilus harrisii	ENSSHAG00000017349	1 retrocopy	retro_shar_827,
Sus scrofa	ENSSSCG00000021408	1 retrocopy	retro_sscr_996,
Tupaia belangeri	ENSTBEG00000012114	1 retrocopy	retro_tbel_3510,
Takifugu rubripes	ENSTRUG00000003009	1 retrocopy	retro_trub_23,