RetrogeneDB ID: retro_ocun_904

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:16391730..16392465(+)
• Located in intron of: ENSOCUG00000013678

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIAL1
• Ensembl ID: ENSOCUG00000003783
• Aliases: None
• Description: TIA1 cytotoxic granule-associated RNA binding protein-like 1 [Source:HGNC Symbol;Acc:11804]

Sequence

>retro_ocun_904
GTTAAAGACATGGCAGTGGGAAAATCCAAACACTGTGGTTTTGTGTCTTTTTATAATAAACTGGATACAGAAAATGCAGT
TGTACATATGGGAGGTCAGTGGTTGGGTGGTAGTCAAATCAGAGCTAACTGGACCACATGTAAACCACCTGCAACTGAAA
GCACACAAGAAAACAACACTAAGCAGTTGATATTTAAAGATGTAGTAAACCAGTCAAGTCCAAAAAACTGTGCTGTGTAC
TGTGGAGGAATTGCTTCTGGGTTAACAGATCAACTTAGGAGAAAGATGTTCTCCCCATTTGGGCAAATTATGGAAAAAAG
TTTTTCTAGAGAAGGGCTATTCATTTGTCAGATTATCAGCCCATGAAAGTGCTGCCCATGCCATTGTTTCAGTGAATAGT
ACTATGATTGAAGGACGTGCAGTTAAATGTTATTGGGGTAAAGAATCTCCTGGTTTGACTAAAAGCTTCCAACAGGTCAA
CTATAGCAGTAGGGCCATTGGAGCCACGTATGTGGAAACCTACAACAGTATGGACAGTATATGGCAAATAGGTGACAAGT
ACTGCCTTAAAGAGTATGTGGGCAATCATGGAATCAATAAGGAAGAGAAGATCAATCACCTTCTGCTGCTTGGATGGGTG
GATTCAGTGCTCAGCCTCTCCAAAGAAAAGCTCCACCCTCTGTAGTACCTCCTCTTAACCAAGCTGGATATGGTATGGTA
GGTTACCAGACACAG

Alignment

ORF - retro_ocun_904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 66.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRKPPAPKSTQENNTKQLRFEDVVN
          VKDMA.GKSK..GFVSFYNKLD.ENA.VHMGGQWLGG.QIR.NW.T.KPPA..STQENNTKQL.F.DVVN
Retrocopy VKDMAVGKSKHCGFVSFYNKLDTENAVVHMGGQWLGGSQIRANWTTCKPPATESTQENNTKQLIFKDVVN

Parental  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG-YSFVRFSTHESAAHAIVSVNGTTIEG
          QSSPKNC.VYCGGIASGLTDQL.R..FSPFGQIME...F...G.YSFVR.S.HESAAHAIVSVN.T.IEG
Retrocopy QSSPKNCAVYCGGIASGLTDQLRRKMFSPFGQIME-KSFSREG>YSFVRLSAHESAAHAIVSVNSTMIEG

Parental  HVVKCYWGKESPDMTKNFQQVDYS-QWGQWSQVYGNPQQYGQYMANGWQVPPYGVYGQPWNQQGFGVDQS
          ..VKCYWGKESP..TK.FQQV.YS.Q.G.WS.V.GN.QQYGQYMAN..QV.P..V.GQ.WNQ.G...DQS
Retrocopy RAVKCYWGKESPGLTKSFQQVNYS<Q*GHWSHVCGNLQQYGQYMANR*QVLP*RVCGQSWNQ*G-REDQS

Parental  PSAAWMGGFGAQPPQGQAPPPVIPPPNQAGYGMASYQTQ
          PSAAWMGGF.AQP.Q..APP.V.PP.NQAGYGM..YQTQ
Retrocopy PSAAWMGGFSAQPLQRKAPPSVVPPLNQAGYGMVGYQTQ

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	58.83 RPM
SRP017611_kidney	0.00 RPM	44.29 RPM
SRP017611_liver	0.00 RPM	20.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_904 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_904 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009888	2 retrocopies	retro_chof_2395, retro_chof_670,
Oryctolagus cuniculus	ENSOCUG00000003783	1 retrocopy	retro_ocun_904 ,
Rattus norvegicus	ENSRNOG00000020271	1 retrocopy	retro_rnor_2547,
Sus scrofa	ENSSSCG00000010685	1 retrocopy	retro_sscr_11,