RetrogeneDB ID: retro_ocun_316

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:150447315..150447774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL49
• Ensembl ID: ENSOCUG00000014882
• Aliases: None
• Description: mitochondrial ribosomal protein L49 [Source:HGNC Symbol;Acc:1176]

Sequence

>retro_ocun_316
GCTCTGTGGAGCTGGAGAGTTGTGTGGCTGGGCTACAGGCTAAAGCCACTGAGCTAGACCCAGGGGCCTCATGATCACCC
CAGCTTTGTAGAATCTGTGGATGAGTACCAGCTTGTGGAGAGCCTGTTATCCCCCATCAGCATCCCCAAACACCCAAAGC
AAGAACATTATCCCATCCTTAGTGGCTGGCAGCCTCCCAGACACATATCGTCCAACCTGCCCTATTCTGTACAGTGTTCT
CAGATGCATAACATCCCTGTCTACAAGGGCATCACACGTGGTAACCGCCAGATGACTGCGATCCAGAAGGTTGAGGGGGA
CATTTGGGGCCTGTGGAAGGATGTGGAAAGGTTTTTTTGAGCCCACTGCTGCAGAAGACACCTCACCTAGGTCAGTGAGA
TGACAGGTACCTTGCGGGTCAAGGGCTACTTTGATGAGCAGCTCAAAGCCCAGCTCCTC

Alignment

ORF - retro_ocun_316 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.58 %
• Parental protein coverage: 92.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVRSWRVGVQPGCGVRPLSQTQGPPGHPSFVESTDEYQFVERLLPPASIPEPPKHERYPTPSGWQPPRDP
          A..SWRV.V..G....PLS.TQGP..HPSFVES.DEYQ.VE.LL.P.SIP..PK.E.YP..SGWQPPR..
Retrocopy ALWSWRV-VWLGYRLKPLS*TQGPHDHPSFVESVDEYQLVESLLSPISIPKHPKQEHYPILSGWQPPRHI

Parental  PPSLPYLVRRSRMHNIPVYKDITHGNRQMTVIRKVEGDIWALQKDVEEFLSPLLGRTPVTQVNEVTGTLR
          ...LPY.V..S.MHNIPVYK.IT.GNRQMT.I.KVEGDIW.L.KDVE.F......R...T.V.E.TGTLR
Retrocopy SSNLPYSVQCSQMHNIPVYKGITRGNRQMTAIQKVEGDIWGLWKDVERFF*AHCCRRHLT*VSEMTGTLR

Parental  VKGYFDEQLKAWLM
          VKGYFDEQLKA.L.
Retrocopy VKGYFDEQLKAQLL

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	14.46 RPM
SRP017611_kidney	0.00 RPM	21.99 RPM
SRP017611_liver	0.00 RPM	15.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_316 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_316 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_316 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012855	1 retrocopy	retro_chof_1006,
Dasypus novemcinctus	ENSDNOG00000004494	6 retrocopies	retro_dnov_1396, retro_dnov_1488, retro_dnov_1941, retro_dnov_2272, retro_dnov_2473, retro_dnov_2686,
Dipodomys ordii	ENSDORG00000003613	1 retrocopy	retro_dord_196,
Homo sapiens	ENSG00000149792	1 retrocopy	retro_hsap_3180,
Macropus eugenii	ENSMEUG00000009437	1 retrocopy	retro_meug_1151,
Microcebus murinus	ENSMICG00000016604	1 retrocopy	retro_mmur_629,
Macaca mulatta	ENSMMUG00000018778	1 retrocopy	retro_mmul_2031,
Nomascus leucogenys	ENSNLEG00000005505	1 retrocopy	retro_nleu_1659,
Oryctolagus cuniculus	ENSOCUG00000014882	1 retrocopy	retro_ocun_316 ,
Pan troglodytes	ENSPTRG00000003867	1 retrocopy	retro_ptro_2263,
Tupaia belangeri	ENSTBEG00000007929	2 retrocopies	retro_tbel_1350, retro_tbel_3334,