RetrogeneDB ID: retro_ocun_875

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:51692770..51693415(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED10
• Ensembl ID: ENSOCUG00000004669
• Aliases: None
• Description: transmembrane emp24-like trafficking protein 10 (yeast) (TMED10), mRNA [Source:RefSeq mRNA;Acc:NM_001082408]

Sequence

>retro_ocun_875
GTCTCTGGTAGCAGGTCTTATTTGCTTAACCTCCTAGCCTGGCATGATCCTTGTCCACTGGTATTGCTGCTTTTGTTCCT
GTTCATCCTAAACTCTGTCCTTACCACCTTTTTCCATCTGTCAACTAACCTTTGCAAATGTCTCTGCAAGAAGTTGCACA
GGGATCTGCTAGTGACAAACCCACACAAGATCATTGTCCAGTCTAGGGTGCAGGGGTTCTGCATACCCAGTTCAAGATCA
CAGATCTTGCTGACCATATTCCATACTACAAGGAGGATGCAACCATGAGGAAATTTGCCTTTACCAATAGAGATTATGAC
ATATCTTAAGTGTGTTTTGAGATCAACGGCCATGGGGGATATTAACCAACGGGTGATCCCAGACATGAAGCGTGGAGTAG
AGATAAAAAAAATTAACAAAGAGGTTGCAAAAGTTGAGAAACTCAAACCATTAGAGGTAAAGTGATGGTGCTTAGAAAAC
CTATCAGAATCTATCATTGATAATTTTGCCTTCATGAAGAAGTGAGAAGGAGATTACACCAGTGAGTCAACAAACACTCA
GATTCTGTATCTCAGCATCTTTTCCATGGTCTGTCTCATTGGTCTAGCCACTTGCCAGTTTTTCAAGGCCAAGAAGTTGC
TGAAA

Alignment

ORF - retro_ocun_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.91 %
• Parental protein coverage: 96.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSGTMSGWSGPLARRGPGPLALLFLFLLGPSSVLAISFHLPVNSRKCLREEIHKDLLVTGAYEITDQSG-
          VSG..S.....LA...P.PL.LL.LFL....SVL...FHL..N..KCL....H.DLLVT....I..QS..
Retrocopy VSGSRSYLLNLLAWHDPCPLVLLLLFLFILNSVLTTFFHLSTNLCKCLCKKLHRDLLVTNPHKIIVQSR<

Parental  GAGGLRTHLKITDSAGHILYSKEDASKGKFAFTTEDYDMFEVCFE-SKGTGRIPDQLVILDMKHGVEAKN
          GAG.L.T..KITD.A.HI.Y.KEDA...KFAFT..DYD...VCFE.S...G.I..Q.VI.DMK.GVE.K.
Retrocopy GAGVLHTQFKITDLADHIPYYKEDATMRKFAFTNRDYDIS*VCFE>STAMGDI-NQRVIPDMKRGVEIKK

Parental  Y-EEIAKVEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIGLATW
          ...E.AKVEKLKPLEV....LE.LSESI...FA.MKK.E.....T.ESTNT..LY.SIFSM.CLIGLAT.
Retrocopy INKEVAKVEKLKPLEVK*WCLENLSESIIDNFAFMKK*EGDY--TSESTNTQILYLSIFSMVCLIGLATC

Parental  QVFYLRRFFK
          Q.F......K
Retrocopy QFFKAKKLLK

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	27.26 RPM
SRP017611_kidney	0.00 RPM	61.32 RPM
SRP017611_liver	0.00 RPM	40.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_875 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_875 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093, retro_mmus_649,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875 ,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,