RetrogeneDB ID: retro_ocun_249

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:112507797..112509012(-)
• Located in intron of: ENSOCUG00000015312

Retrocopy information

• Ensembl ID: ENSOCUG00000015321
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDI2
• Ensembl ID: ENSOCUG00000023891
• Aliases: None
• Description: DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]

Sequence

>retro_ocun_249
ATGCTCGTCACTGTGTACTGTGTGCGGAGGGACCTCTCCGAGGTAACCTTCTCCCTCCAGGTCAGCCCTGACTTTGAACT
CCGTGACTTCCGAGTCCTGTGTGAGACAGAGTCCAGAATCCCTGCCGAAGAGACCCAGTTCATCTACATGGAGCACCTCC
TCGCTGATGACCACTGTTCCCTGGGCTCCTACGGCCTCAAAGACGGTGATGTCATTGTATTACTCCAGAAGGAGAATGTG
GGACCTAGGCTTCCAGGACGGACTCCAAACCAGCCTCGAACAGATTTCAATGGAATCGCCACGCCTGGGACATCAGGCTC
TCGGTGGCAGCAGCAGCAACCCCCTGTGCAGCAAGCGTGTGCGCCTTCTGCTCGTCATTCCCACGGCTTGGCCTCTGGAG
AGAAGATGGCATCTGCTCAAGGTCTGGACAGCCCAGCCTTGATCCGTAGCATGCTGCTGTCCAATCCTCACGACCTGTCC
CTGCTGAAGGAACGCAACCCTTCCTTGGCAGAAGCTCTGCTCAGCGGGAACCTTGAAACATTTTCTCAGGTCTTGATGGA
GCAGCAGAGGGAGAGAGCCTTGCGAGAGCAAGAGAGGCTTCGTCTCTACTCCGCGGACCCATTTGATAGGGAAGCTCAGG
CCAAAATAGAAGAAGAAATCCGGCAGCAGAACATTGAAGAAAACATGAATATAGCAATGGAAGAGGCCCCCGAGAGTTTT
GGGCAAGTGGCAATGCTCTACATCAACTGCAAAGTGAATGGACATCCTTTGAAGGCTTTTGTTGACTCGGGTGCCCAGAT
GACCATTATGAGCCAAGCGTGTGCGGAGAGATGCAACATCATAAGACTGGTGGACCGACGATGGGCTGGAGTGGCTAAAG
GAGTGGGCACACAAAGAATCATCGGCCGCGTTCATTTAGCTCAAATTCAGATTGAAGGAGACTTCCTGCAATGTTCTTTC
TCTATACTTGAGGAGCAGCCCATGGACATGCTTCTCGGACTAGATATGCTGAAGAGGCATCAGTGTTCCATCGATTTGAA
GAAAAATGTGCTGGTGATTGGCACCACTGGCACACAGACATCCTTTCTTCCTGAGGGAGAGTTACCCCCCTGTGCTAAGC
TGGTAAGTGTTACCGGGCAAGAAGAGCCTTCAGACAAGGACACGGCAAACACCATTAAGCATTCACTCAAGGATTCAGGA
CGAAAGAAGCACTGA

Alignment

ORF - retro_ocun_249 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.67 %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VYAERPLTDNHRSLASYGLKDGDVVILRQKENADPRPPVQFPSLPRIDFSSIAVPGTSSPR---QRPPA-
          .Y.E..L.D.H.SL.SYGLKDGDV..L.QKEN..PR.P...P..PR.DF..IA.PGTS..R...Q.PP..
Retrocopy IYMEHLLADDHCSLGSYGLKDGDVIVLLQKENVGPRLPGRTPNQPRTDFNGIATPGTSGSRWQQQQPPVQ

Parental  -AVKPS--HSSG----EMAASPQGLDNPALLRDMLLANPHELSLLKERNPPLAEALLSGDLERFSRVLVE
          .A..PS..HS.G....E..AS.QGLD.PAL.R.MLL.NPH.LSLLKERNP.LAEALLSG.LE.FS.VL.E
Retrocopy QACAPSARHSHGLASGEKMASAQGLDSPALIRSMLLSNPHDLSLLKERNPSLAEALLSGNLETFSQVLME

Parental  QQQDRARREQERIRLFSADPFDLEAQAKIEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPV
          QQ..RA.REQER.RL.SADPFD.EAQAKIEE.IRQQNIEENM.IAMEEAPESFGQV.MLYINCKVNGHP.
Retrocopy QQRERALREQERLRLYSADPFDREAQAKIEEEIRQQNIEENMNIAMEEAPESFGQVAMLYINCKVNGHPL

Parental  KAFVDSGAQMTIMSQACAERCNIMRLVDRRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSFSILEEQP
          KAFVDSGAQMTIMSQACAERCNI.RLVDRRWAG.AKGVGTQ.IIGRVHLAQ.QIEGDFL.CSFSILEEQP
Retrocopy KAFVDSGAQMTIMSQACAERCNIIRLVDRRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLQCSFSILEEQP

Parental  MDMLLGLDMLKRHQCSIDLKKNVLVIGTTGSQTTFLPEGELPECARLAYGAVRPEEIADQELAEAIQKSA
          MDMLLGLDMLKRHQCSIDLKKNVLVIGTTG.QT.FLPEGELP.CA.L.......EE..D...A..I..S.
Retrocopy MDMLLGLDMLKRHQCSIDLKKNVLVIGTTGTQTSFLPEGELPPCAKLV-SVTGQEEPSDKDTANTIKHSL

Parental  EDAERQK
          .D..R.K
Retrocopy KDSGRKK

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	4.25 RPM
SRP017611_kidney	0.00 RPM	9.93 RPM
SRP017611_liver	0.00 RPM	14.80 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_249 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_249 has 11 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_96
Pan troglodytes	retro_ptro_570
Gorilla gorilla	retro_ggor_143
Pongo abelii	retro_pabe_158
Macaca mulatta	retro_mmul_231
Callithrix jacchus	retro_cjac_196
Mus musculus	retro_mmus_67
Bos taurus	retro_btau_15
Sus scrofa	retro_sscr_6
Canis familiaris	retro_cfam_193
Equus caballus	retro_ecab_110

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15, retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249 ,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,