RetrogeneDB ID: retro_ocun_1827

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019115:89220..89993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf41
• Ensembl ID: ENSOCUG00000017017
• Aliases: None
• Description: chromosome 9 open reading frame 41 [Source:HGNC Symbol;Acc:23435]

Sequence

>retro_ocun_1827
AAGCCAAGGATGGTGGCAGGGATGCAGCAGAGGAGTTTAGCACAGCTTCCCGCCACTCAGCTGCCAAAGGCTGCTGGCCA
GAAAGCAGCGGCAGCTGTGCTGGAAGTGGTGTGGTGGAATCACTGTTCTCCACCCTGCACTGGGGCTCGGCCATGGCGAT
GTCCTCAGCTGCCTTGAGCAGCATGGAGGAGGAAAAGGACAGGCTGGAGCACTAGCAATTCTGGAAGATCACAAATGCTC
TCAGCCACTATGGCCCCAGAATGTAAGAGTTGGCACATTGAATAGAAAGAGAATTTTGATCACTTCCAGTTAATCAGCAG
AAACTGCTTCCTCAATATCTTAACTTTGACAAGATCTCAAACTGCATTGATCCTAATCAAGACATGCTACTGACCATTGT
GAACGACTTTATAAATATGTTTGGAAATAAAGGATATGGAGAATATGGAAAGAATGGAAAGATTTAGACAGCATCTACAC
TTCACATGAAAGTTAAAATCCCATACTGAGACACTTTGTGAGACTGTAGTGAAACTGGCGAAGCAGGATGGGATTCCTGC
TACCAGCCAATCATTATAAAAATGTTTTTTAAATTTTCCGAGATATGGGATCCTTCAAAAACAAATATTCCGGTACATGG
TGCTAGACTAGAAAGATTGGTCTGGAAAATATCTCTGCTAGGTTGTGAGTGCCAAGGAAAGGAATGGACACTTTTGTGCT
TTTCCCCAAGGTTTATACTAGAAAGATGCTCTGAAATTAACAAACTTTATCCC

Alignment

ORF - retro_ocun_1827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 57.02 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPRAAAAMQRRRRPPPPASQLPE-GCGGSGGGGGRGGSEEVEVQFSAGRLGSAAAVSSTAARSTEEEEER
          .PR..A.MQ.R.....PA.QLP..GC.....G....GS..VE..FS....GSA.A.SS.A..S.EEE..R
Retrocopy KPRMVAGMQQRSLAQLPATQLPK<GCWPESSGSC-AGSGVVESLFSTLHWGSAMAMSSAALSSMEEEKDR

Parental  LEREHFWKIINAFRYYGTSMHERVHRTERQFRSLPPNQQKLLPQFVLHLDKIRKCIDHNQEILLTIVNDC
          LE...FWKI.NA...YG..M.E..H..ER.F.SLP.NQQKLLPQ..L..DKI..CID.NQ..LLTIVND.
Retrocopy LEH*QFWKITNALSHYGPRM*ELAH*IEREF*SLPVNQQKLLPQY-LNFDKISNCIDPNQDMLLTIVNDF

Parental  IHMFENKEYGEDG-NGKIMPASTFDMDKLKSTLKQFVRDWSETGKAERDACYQPIIKEILKNFPKERWDP
          I.MF.NK.YGE.G.NGKI..AST..M.K.K........D.SETG.A..D.CYQPII......F..E.WDP
Retrocopy INMFGNKGYGEYGKNGKI*TASTLHM-KVKIPY*DTL*DCSETGEAGWDSCYQPIIIKMFFKF-SEIWDP

Parental  SKVTILVPGAGLGRLAWEIAMLGYACQGNEWSFFMLFSSNFVLNRCSEINKYRLYP
          SK..I.V.GA.L.RL.W.I..LG..CQG.EW.....FS..F.L.RCSEINK..LYP
Retrocopy SKTNIPVHGARLERLVWKISLLGCECQGKEWT-LLCFSPRFILERCSEINK--LYP

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	9.49 RPM
SRP017611_kidney	0.00 RPM	14.29 RPM
SRP017611_liver	0.00 RPM	5.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1827 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1827 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024726	2 retrocopies	retro_mmus_1013, retro_mmus_3359,
Oryctolagus cuniculus	ENSOCUG00000017017	4 retrocopies	retro_ocun_1659, retro_ocun_1737, retro_ocun_1827 , retro_ocun_921,
Ictidomys tridecemlineatus	ENSSTOG00000000385	5 retrocopies	retro_itri_1389, retro_itri_1652, retro_itri_1653, retro_itri_1654, retro_itri_1843,