RetrogeneDB ID: retro_ocun_435

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:28954179..28954799(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C18orf21
• Ensembl ID: ENSOCUG00000028046
• Aliases: None
• Description: chromosome 18 open reading frame 21 [Source:HGNC Symbol;Acc:28802]

Sequence

>retro_ocun_435
AAGCAGATAGACCAACTTGTTGCTGTGGTGTGGAAACTACCTGACAGCTTCCCGGGCCAGGCCTGCTGTCTGCCCTGGGC
CTCAGTTCATCACATGAAGATAGAAATTTTGAAGAAACTCGTCCATACTGTTTCCTTTTGTTGGTTCTGGCTAATTCTTG
AGTGTACCTTAAACCCAAGGCCAAACTGACACTCAAAATACAAACCTCTCTTAATTGAGAAGAAATTCTACATTCAATTT
TAAAGAAGCACATTGTGAAAAAGCATGAAGACAATGGAAGTGTGTTGTTAATGACTTGTAACACCTGCAACAGGACAGGG
AAACGTGGAGAAAGCAGCTTGCCATCAGCAATGAAGAACAACCCCACCATGCAATGAGCAACCTAACCAGAAAATAAGAG
AGAAAGACTCCAAATGCAGTGAACCCAGATCTGTCTGGCTCTGAAGGCAAGAGCACATCACTGATCTTTGGAATACCTAC
CTCTACACAGTCAGCACCCATCTGCTCCCCAAAGAATGTGAGCAAAACAAAAAACCTCTCTCTCAACTGAAAACATTGCT
CAGCAAGAATGAATCCCAAGAGAATCCAAAGTGCATTTCAGAAATTTCTTATCTTCTCTT

Alignment

ORF - retro_ocun_435 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.72 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RQKHYLEAAARKLHSSCPGQARYLLWA-YGSSHDDKSNFEETCPYCFQLLVLDNSRVRLKPKAKLTPKIQ
          .Q...L.A...KL..S.PGQA..L.WA...SSH.D..NFEET.PYCF.LLVL.NS.V.LKPKAKLT.KIQ
Retrocopy KQIDQLVAVVWKLPDSFPGQACCLPWA<LSSSHEDR-NFEETRPYCFLLLVLANS*VYLKPKAKLTLKIQ

Parental  KLLNREARNFTLSFKEAKILKKYRDSKSVLLVTCKTCNRAVQHPGKSRSFLSALKSS-PSTPLSKLSQEI
          ..LN.E......S.....I.KK..D..SVLL.TC.TCNR.....G.S.S..SA.K...P....S.L....
Retrocopy TSLN*E--EILHSILKKHIVKKHEDNGSVLLMTCNTCNRTGKR-GES-SLPSAMKNN<PHHAMSNLTRK*

Parental  AERRTPNAVNLTLSASRGKSPALTFRTPTSGQSTPICSPKNVSRT-KKHLSQLKMLLSKSESQENP-KMD
          .ER.TPNAVN..LS.S.GKS..L.F..PTS.QS.PICSPKNVS.T.KK.LSQLK.LLSK.ESQENP.K..
Retrocopy -ERKTPNAVNPDLSGSEGKSTSLIFGIPTSTQSAPICSPKNVSKT<KKPLSQLKTLLSKNESQENP<KVH

Parental  FRNFLSSL
          FRNFLSSL
Retrocopy FRNFLSSL

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	19.76 RPM
SRP017611_kidney	0.00 RPM	21.28 RPM
SRP017611_liver	0.00 RPM	4.24 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_435 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_435 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029548	1 retrocopy	retro_cfam_1636,
Callithrix jacchus	ENSCJAG00000021041	2 retrocopies	retro_cjac_1030, retro_cjac_2169,
Cavia porcellus	ENSCPOG00000025449	1 retrocopy	retro_cpor_1461,
Felis catus	ENSFCAG00000000626	1 retrocopy	retro_fcat_1717,
Homo sapiens	ENSG00000141428	1 retrocopy	retro_hsap_3062,
Gorilla gorilla	ENSGGOG00000026334	1 retrocopy	retro_ggor_2102,
Macaca mulatta	ENSMMUG00000018782	1 retrocopy	retro_mmul_1876,
Monodelphis domestica	ENSMODG00000025605	1 retrocopy	retro_mdom_260,
Mus musculus	ENSMUSG00000024273	2 retrocopies	retro_mmus_1676, retro_mmus_610,
Nomascus leucogenys	ENSNLEG00000006237	1 retrocopy	retro_nleu_1655,
Oryctolagus cuniculus	ENSOCUG00000028046	2 retrocopies	retro_ocun_1910, retro_ocun_435 ,
Ochotona princeps	ENSOPRG00000011163	2 retrocopies	retro_opri_1222, retro_opri_283,
Pongo abelii	ENSPPYG00000009110	1 retrocopy	retro_pabe_2536,
Pan troglodytes	ENSPTRG00000009973	2 retrocopies	retro_ptro_1981, retro_ptro_2935,
Pteropus vampyrus	ENSPVAG00000009174	3 retrocopies	retro_pvam_1086, retro_pvam_1488, retro_pvam_629,
Tupaia belangeri	ENSTBEG00000016670	1 retrocopy	retro_tbel_4056,
Tarsius syrichta	ENSTSYG00000010817	2 retrocopies	retro_tsyr_1675, retro_tsyr_1787,