RetrogeneDB ID: retro_ocun_312

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:143443968..143444571(+)
• Located in intron of: ENSOCUG00000010457

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSOCUG00000009785
• Aliases: None
• Description: Serine/arginine-rich splicing factor 6 [Source:UniProtKB/Swiss-Prot;Acc:O18776]

Sequence

>retro_ocun_312
CGCAGTGCTGGGGGTGGAGACAGCAGTCGGAGAGCCTCTGGTGGAGACAGATGTGGACTGCCTGTTTATGTGGGATACAG
GCTAATTGTAGAAAATCCTTTTAGTCGGTGCAGTTGGCAAGATTCAAAAGATTTTATGTGGCAAGCAGGTGAAGTAACTG
AGGTGGATGCTCACAGAGAATGCACAAATGAGGTTGTAATTGAATTGTGCTCTTACTGGGACACGAAGTGTGCTGTGGAT
AAAATGGATAGTACAGAAATAAATGGCAGAAATGTTAGCCTTGTTGAAGATGAGCCCTGAGAGAACCATGGGCGATCTTA
CCAGGGAAGCAGATCCAGGTCATGGTGTAGAAGACCAGCAGGTAGGAGTTGCAGGAGCATCCGCAGTAGATCTACCTGGA
AATATGTTAAAAAGCCACTCCCAATCCAGGTTTCAGAGCAAAGATCCATCACAAGGCAGGAAATGCAGATCAGAGAGCAA
ACCTAAACCCAAGTCTGATCGGGGCTTCCGTTCACATTCTCGGAGTGGATCTAAGATGCATCTGAGCAGGCCCAAAGCAG
ACCTCAGTCTTTAGCTCTGTCCCCCAAAGAAAATGGAAAAGGG

Alignment

ORF - retro_ocun_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.0 %
• Parental protein coverage: 68.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGGGGGYSSRRTSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERTNEGVIEFR
          ...GGG.SSRR.SG.D..G.PV...YRLIVEN..SRCSWQD.KDFM.QAGEVT..DAH.E.TNE.VIE..
Retrocopy RSAGGGDSSRRASGGDRCGLPVYVGYRLIVENPFSRCSWQDSKDFMWQAGEVTEVDAHRECTNEVVIELC

Parental  SYSDMKRALDKLDGTEINGRNIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRSRRSSR-SRSRSISKSR
          SY.D.K.A.DK.D.TEINGRN..L.ED.P...H.RSY.G....SRSR...R....RS.R...........
Retrocopy SYWDTKCAVDKMDSTEINGRNVSLVEDEP*ENHGRSYQG----SRSRSWCRRPAGRSCR>ASAVDLPGNM

Parental  SRSRSRSKGRSRSRSKGRKSRSKSKSKPKSDRGSRSRSRSRSK-DEYEKSRSRSRSRSRSPKENGKG
          ..S.S.S...S...S.GRK.RS.SK.KPKSDRG.RS.SRS.SK.D..E...SR..S...SPKENGKG
Retrocopy LKSHSQSRFQSKDPSQGRKCRSESKPKPKSDRGFRSHSRSGSK<DASEQAQSRPQSLALSPKENGKG

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	89.57 RPM
SRP017611_kidney	0.00 RPM	102.57 RPM
SRP017611_liver	0.00 RPM	52.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_312 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_312 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Nomascus leucogenys	ENSNLEG00000006524	1 retrocopy	retro_nleu_1294,
Oryctolagus cuniculus	ENSOCUG00000006684	3 retrocopies	retro_ocun_415, retro_ocun_772, retro_ocun_970,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312 ,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,