RetrogeneDB ID: retro_ocun_1737

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018830:353909..354620(-)
• 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_1737
ACCGCCGCGCGCAGTGCAGCCCAGAACAGGAGAGGCTTGAGCACTAGCACTTCTGGAAGATCATTAATGCCTTCAGCTAC
TAGGGCACCAGTATGCATGAGCGAGAACAACGAACAGAAAGACAGTTTCAGTCACTTCCACCTAATCAGCAGAAACTACT
TCCTCAATTTCTTCTACATTTGGAAAAGATCTGAAAATGCATTGATCATAATCAAGAAATACTACTGACAGTTGTGAATG
ACTGCATGCGTATGTTTGAAAATAAAGAATATGAAAAAGATGGGAATGGAAAGATTAGGGCAGCATCTACCTTTGACATG
GATAAGTTACAATCCACATTGAAACAGTTTGTGAGAGACTGGAGAAAAACTGGGAAAGCAGAAAGGGATACCTGCTACCA
GCTAATCATTAAGGAAATTTTTAAAATTTTTCCAAGGAGAGGTGGAATCCTTCTAAAGAAATGAATCTGGTACCTGGTGC
TGCACTAGGAAGACCGGCCTGTAAAGTAGCTGTGCTAGGTTACGCTTGTCAAGGAAATGAACGGAGTTTTTTATGCTCTT
TTCTTCCAACTTTGTATTCAGCAGATGCTCTGAAATTAGTAAATACAAACATTATCCCTGGATCCACCAAAATAGCAATA
AATGGAGATTGGCTGATCAGATTCAACCCATCTTCTTCCCCCATGTTGACACCCCCCCCCAGTCTTCCTTC

Alignment

ORF - retro_ocun_1737 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.49 %
• Parental protein coverage: 52.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAARSTEE-EEERLEREHFWKIINAFRYYGTSMHERVHRTERQFRSLPPNQQKLLPQFVLHLDKIRKCID
          TAARS....E.ERLE.................MHER..RTERQF.SLPPNQQKLLPQF.LHL.KI.KCID
Retrocopy TAARSAAQ<EQERLEHXXXXXXXXXXXXXXXXMHEREQRTERQFQSLPPNQQKLLPQFLLHLEKI*KCID

Parental  HNQEILLTIVNDCIHMFENKEYGEDGNGKIMPASTFDMDKLKSTLKQFVRDWSETGKAERDACYQPIIKE
          HNQEILLT.VNDC..MFENKEY..DGNGKI..ASTFDMDKL.STLKQFVRDW..TGKAERD.CYQ.IIKE
Retrocopy HNQEILLTVVNDCMRMFENKEYEKDGNGKIRAASTFDMDKLQSTLKQFVRDWRKTGKAERDTCYQLIIKE

Parental  ILK-NFPKERWDPSKVTILVPGAGLGRLAWEIAMLGYACQGNEWS-FFMLFSSNFVLNRCSEINKYRLYP
          I.K.NF.KERW.PSK...LVPGA.LGR.A...A.LGYACQGNE.S.FFMLFSSNFV..RCSEI.KY..YP
Retrocopy IFK<NFSKERWNPSKEMNLVPGAALGRPACKVAVLGYACQGNERS<FFMLFSSNFVFSRCSEISKYKHYP

Parental  WIHQFSNNRRSADQIRPIFFPDVDPHSLPPGSNF
          WIHQ.SN..R.ADQI.PIFFP.VD....PP.S.F
Retrocopy WIHQNSNKWRLADQIQPIFFPHVD---TPPQSSF

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_1737 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1737 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1737 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,