RetrogeneDB ID: retro_ocun_675

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:137159292..137159753(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL13
• Ensembl ID: ENSOCUG00000016189
• Aliases: None
• Description: mitochondrial ribosomal protein L13 [Source:HGNC Symbol;Acc:14278]

Sequence

>retro_ocun_675
AAAATGCAGACCCCTGGCAAATTGGCTGCTATAGCATCAGTAAAACTTCATGGATTACATAAACATATATACCTTGAACT
GAGTGGCTGTGGCAGTCATGCTGTCATAATGAACACAAGTCACAGTGCATTTGTTGGAAACAAACAGGAACAAAAAATGA
AATCCTCACATAGCAGTTACCCAGGTAGGTTTAGAAGAGTAACTCGTACTGAATTTCACCAGAAGGATCCAGTGGCAACC
ATAAAATTGGCTATTTATGACATGCTGCCCCCAAACCCTCACAGAACAGTAAGGCAATGGCTACAACTTTTCTATATGAG
AATATTCTAGAAGATATCCTTAAGGATTTAGTGGAAGAGCTTCCTCGACCACGAAAAGTACCTAGACGCCTTGATGAGTA
CACACAAGAAGAAACAGGGGCTTCCCCAAGAGTGTGGTCTCCCCTCGAAGATTATCTGCTA

Alignment

ORF - retro_ocun_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 87.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMQPPGKLAAVASMKLQGLHKPIYHQLSDCGDHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFRQVTAA
          KMQ.PGKLAA.AS.KL.GLHK.IY..LS.CG.H.VIMNT.H.AF.GNK.EQK..SSH..YPG.FR.VT..
Retrocopy KMQTPGKLAAIASVKLHGLHKHIYLELSGCGSHAVIMNTSHSAFVGNKQEQKMKSSHSSYPGRFRRVTRT

Parental  ELHQKDPVAIVKLAIYGMLPKNLHRRTMMQRLHL-FPDENIPEDILKNLVEEIPQPRKVPKRLDEYTQEE
          E.HQKDPVA..KLAIY.MLP.N.HR.T..Q.L.L.F..ENI.EDILK.LVEE.P.PRKVP.RLDEYTQEE
Retrocopy EFHQKDPVATIKLAIYDMLPPNPHR-TVRQWLQL<FLYENILEDILKDLVEELPRPRKVPRRLDEYTQEE

Parental  VEAFPRIWSPPEDYRL
          ..A.PR.WSP.EDY.L
Retrocopy TGASPRVWSPLEDYLL

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	8.17 RPM
SRP017611_kidney	0.00 RPM	15.81 RPM
SRP017611_liver	0.00 RPM	4.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_675 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_675 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	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675 ,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274, retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,