RetrogeneDB ID: retro_ocun_1352

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:33119608..33120410(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000022143
• Aliases: None
• Description: None

Sequence

>retro_ocun_1352
TTAGCTGGGAATGTGTAACACAGAAGTGCATGCACACTACTAAACCAGGTCCCAGATGTGCTACATAGATTTCTATGGAA
AGAACTCTGTCTGTACAGCATTTAGATTCAAAGGAAAGCCAGGAAATGCAGTGTATGGACAAAAAGAAATCCACGGGAAA
ATGATGTCACAAAACTTCCCCACCTGCCACAGCAAGGTCTGCCATATTGATGCTCATGCTGCTTCAAAATGATGTGATGG
TGCAGGTGATGGAACTGCTCTCTAGCAACAACCAAGCTTTAAGGAGATTCCTCAATCATTTGTCCTTGCTCCTGAGGGCT
CTGTTGCAAGGAAGTTTTGTGTTCACAATTGTACCTTCAGATACCAAGATGAGGTCATTCATGGCTTTGTCTCTGATCCT
CAGGAATAATCTGGGGATGACATAGAGAAACCTGAAGAAAGAGAGCAGGCTCCTGAAGTGGTCCCCGATGATTCATGAGC
TTTCTGTGATCAGACTGTCAGCAATGACTTGGAAGCACATTTAGAGGAGCCTGTTAGTGAACTAGAGCCTGATCCTGAAC
CAGAAGCAGAACAAGAATCTGTCTCTGAAATCCAAGAGTAAAAGTCTGAGCCAGTATTGTAAGGAACTACTACCAAAAAT
GCTCAGAAGAGTTATTCTCCAGCACCCACAGATGTAATGTAGGCACTATAGGAAGACTAGAAGACATTTGCTTGGGCATC
TGTGACCAGTAAGACTCTTTCACCCTGTGGAGCTATTCCTGTTACTGGGATAACAGTTCATGTTACTTAAGTTCCAGCTG
CA

Alignment

ORF - retro_ocun_1352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.64 %
• Parental protein coverage: 59.13 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LVGREFVRQYYTLLNQAPDMLHRF-YGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIR
          L.G....R...TLLNQ.PD.LHRF.YGKNS..V.......GKP..AVYGQKEIH.K.MSQNF..CH.K..
Retrocopy LAGNV*HRSACTLLNQVPDVLHRF>YGKNS--VCTAFRFKGKPGNAVYGQKEIHGKMMSQNFPTCHSKVC

Parental  HVDAHAT-LNDGVVVQVMGLLSNNNQALRRFM-QTFVLAPEGSVANKFYVHNDIFRYQDEVFGGFVTEPQ
          H.DAHA...ND.V.VQVM.LLS.NNQALRRF..Q.FVLAPEGSVA.KF.VHN..FRYQDEV..GFV..PQ
Retrocopy HIDAHAA>QND-VMVQVMELLSSNNQALRRFL<QSFVLAPEGSVARKFCVHNCTFRYQDEVIHGFVSDPQ

Parental  EESEEEVEEPEERQQTPEVVPDDSGTFYDQTVSISNFITTHLTFLFCCVRISCESNDLEEHLSEIQEEKP
          E.S....E.PEER.Q.PEVVPDDS..F.DQTV..SN....HL...........E.....E..SEIQE.K.
Retrocopy E*SGDDIEKPEEREQAPEVVPDDS*AFCDQTV--SNDLEAHLEEPVSELEPDPEPEAEQESVSEIQE*KS

Parental  EPVLEEATPEDAQKSSSPAPADIAQTAQEDLRTFSWASVTSKNLPPSGAVPVTGIPPHVVKVPAS
          EPVL...T...AQKS.SPAP.D......ED..TF.WASVTSK.L.P.GA.PVTGI..HV..VPA.
Retrocopy EPVL*GTTTKNAQKSYSPAPTDVM*AL*ED*KTFAWASVTSKTLSPCGAIPVTGITVHVT*VPAA

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	6.51 RPM
SRP017611_kidney	0.00 RPM	18.04 RPM
SRP017611_liver	0.00 RPM	14.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1352 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1352 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1352 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006626	2 retrocopies	retro_cpor_1119, retro_cpor_464,
Dasypus novemcinctus	ENSDNOG00000018758	3 retrocopies	retro_dnov_1492, retro_dnov_1632, retro_dnov_526,
Echinops telfairi	ENSETEG00000017447	1 retrocopy	retro_etel_1488,
Homo sapiens	ENSG00000145907	1 retrocopy	retro_hsap_2322,
Microcebus murinus	ENSMICG00000012235	2 retrocopies	retro_mmur_1247, retro_mmur_1469,
Mustela putorius furo	ENSMPUG00000013661	1 retrocopy	retro_mputfur_625,
Mus musculus	ENSMUSG00000018583	3 retrocopies	retro_mmus_1389, retro_mmus_3229, retro_mmus_3688,
Nomascus leucogenys	ENSNLEG00000016470	1 retrocopy	retro_nleu_1814,
Oryctolagus cuniculus	ENSOCUG00000022143	1 retrocopy	retro_ocun_1352 ,
Otolemur garnettii	ENSOGAG00000001726	2 retrocopies	retro_ogar_3156, retro_ogar_3183,
Pongo abelii	ENSPPYG00000015968	1 retrocopy	retro_pabe_2104,
Pan troglodytes	ENSPTRG00000017438	1 retrocopy	retro_ptro_1696,
Pteropus vampyrus	ENSPVAG00000017250	2 retrocopies	retro_pvam_1188, retro_pvam_188,
Rattus norvegicus	ENSRNOG00000013186	1 retrocopy	retro_rnor_1282,
Tupaia belangeri	ENSTBEG00000004386	12 retrocopies	retro_tbel_2177, retro_tbel_2295, retro_tbel_2296, retro_tbel_2327, retro_tbel_2352, retro_tbel_2460, retro_tbel_2461, retro_tbel_3889, retro_tbel_3928, retro_tbel_4180, retro_tbel_4190, retro_tbel_4246,
Tarsius syrichta	ENSTSYG00000004570	1 retrocopy	retro_tsyr_1391,
Tursiops truncatus	ENSTTRG00000009072	1 retrocopy	retro_ttru_70,