RetrogeneDB ID: retro_ocun_630

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:3332576..3333159(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL4
• Ensembl ID: ENSOCUG00000008794
• Aliases: None
• Description: ribosomal protein L4 [Source:HGNC Symbol;Acc:10353]

Sequence

>retro_ocun_630
GTCTACTCCTGAAGAGAAGAGTAATCTGGCAAAAACATCGCTTTATCTTCTGTGCCAAAGGTTCCCATTCTGTGGGATAA
GTGAACTTTTTTCACACCAGCTTGCATAAAAACACCAGGCAGCCCCATGCTGTCAGTGAATTAGCAGGTCACCGACCACT
GCTGGGTCTTGGAGTACTGGCAGAGCTGTGGCTCAAGTTCTCATCGTCTGAGGCAGTGGAACTCATTGATCCGTCCAGGG
TGCTTTTGGAAATCTGTGCCAAAGAGGTTGCATATTTGTAACAACCAAAGCTTGGTGCCATTGGCATTATGGCATTTACA
CAATCCAAGAGTGACAAGCCATCTGCTCTGCCCTGGCTGTATCAGCCTTGCCAGCACTGGTAATGTCTAAAGGCAATGTA
TTGAGGAAGTTCCTTAACATCATACTGGTGGTTGAAGATAAAGTTGAAGGTTACAAAAAGATCAAGGAGGCTGTTTTGCT
GCTTCAGACTCTTAAGGCCTGGCATGACATCAAAAATGTCTATGCCTCTCAGAGAGCTGGCAAGGGCACAAGAAGAAGCC
AGCAAGGAATCCAGCACAAGGGC

Alignment

ORF - retro_ocun_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.81 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VYSEKGESSGKNVTLPAVFKAPIRPDI-VNFVHTNLRKNNRQPYAVSELAGHQ-TSAESWGTGRAVARIP
          VYS...E.SGKN..L..V.K.PI..D..VNF.HT.L.KN.RQP.AVSELAGH..T.A.SW.TGRAVA...
Retrocopy VYS*REE*SGKNIALSSVPKVPILWDK<VNFFHTSLHKNTRQPHAVSELAGHR<TTAGSWSTGRAVAQVL

Parental  RVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEV
          .V.G.GTH.S.QGAFGN.C..G..F..TK.W..WH....T.Q...AICSALA.SALPALVMSKG......
Retrocopy IV*GSGTH*SVQGAFGNLCQRGCIFVTTKAWCHWHYGIYTIQE*QAICSALAVSALPALVMSKGNVLRKF

Parental  PELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRG
          ....LVVEDKVEGYKK.KEAVLLL..LKAW.DIK.VYASQ..RAGKG..R....IQ..G
Retrocopy LNIILVVEDKVEGYKKIKEAVLLLQTLKAWHDIKNVYASQ--RAGKGTRRSQQGIQHKG

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	499.23 RPM
SRP017611_kidney	0.00 RPM	744.97 RPM
SRP017611_liver	0.00 RPM	394.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_630 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_630 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005211	2 retrocopies	retro_btau_101, retro_btau_610,
Canis familiaris	ENSCAFG00000017309	1 retrocopy	retro_cfam_72,
Callithrix jacchus	ENSCJAG00000007491	2 retrocopies	retro_cjac_251, retro_cjac_945,
Cavia porcellus	ENSCPOG00000003055	1 retrocopy	retro_cpor_370,
Echinops telfairi	ENSETEG00000000337	3 retrocopies	retro_etel_1876, retro_etel_2195, retro_etel_226,
Felis catus	ENSFCAG00000012293	4 retrocopies	retro_fcat_1136, retro_fcat_189, retro_fcat_505, retro_fcat_567,
Gorilla gorilla	ENSGGOG00000003695	4 retrocopies	retro_ggor_1023, retro_ggor_2008, retro_ggor_2831, retro_ggor_304,
Myotis lucifugus	ENSMLUG00000011809	2 retrocopies	retro_mluc_121, retro_mluc_198,
Macaca mulatta	ENSMMUG00000016844	2 retrocopies	retro_mmul_2160, retro_mmul_649,
Monodelphis domestica	ENSMODG00000009657	2 retrocopies	retro_mdom_656, retro_mdom_944,
Mustela putorius furo	ENSMPUG00000000337	3 retrocopies	retro_mputfur_1205, retro_mputfur_411, retro_mputfur_570,
Mus musculus	ENSMUSG00000032399	2 retrocopies	retro_mmus_2863, retro_mmus_495,
Nomascus leucogenys	ENSNLEG00000012938	4 retrocopies	retro_nleu_1041, retro_nleu_1062, retro_nleu_2385, retro_nleu_887,
Oryctolagus cuniculus	ENSOCUG00000008794	3 retrocopies	retro_ocun_1134, retro_ocun_630 , retro_ocun_631,
Ochotona princeps	ENSOPRG00000007792	1 retrocopy	retro_opri_735,
Pongo abelii	ENSPPYG00000006578	1 retrocopy	retro_pabe_152,
Rattus norvegicus	ENSRNOG00000009378	5 retrocopies	retro_rnor_1192, retro_rnor_1621, retro_rnor_2061, retro_rnor_2484, retro_rnor_949,