RetrogeneDB ID: retro_ocun_631

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:12726628..12727546(-)
• 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_631
GCCGCCGGGAGGAGAGGAGCGTGGCTCTCACCTCTCCCCGCCATGGCGTGTGCTCGTCCTCTCCTATCGGTGTACTCCGA
GAAGGGGGAGTCGTCCGGCAAAAATGTGACTTTGCCCGCCATGTTCAAGGCTCCCATCCAGCCAGACATCGTGAACTTCG
TGCACACCAACGTGCGCAAGAACAATAGGCAGCCCTATGCCGTCAGTGAGCTGGCAGGTCACCAGACCAGCGCTGAGTCG
TGGGGTACTGGCAGAGCTGTGGCGGGAATTCCCAGAGTGCGAGGTGGTGGGACGCACCGATCCGGCCAGGGTGCCTTTAG
GAATATGTGCCGAGGAGGCCGCATGTTCGCACCAACCAAAACCTGGTGCCATTGGCACCGGCGAGTGAACACGACCCAGA
AGTGGTACGCCATCTGCTCTGCCCTAGCTGCGTTGGCCTTGCCAGCACTGGTCATGTCTAAAGGTCATGGTATTGAGGAA
GTGCCGGAACTTCCTCTGGTGGTCGAAGATAAGGTTGAAGGCTACAAGAAGACCAAGGAGGCAGTTCTGCTGCTTAAGAA
ACTCAAGGCCTGGAATGACATCAAGAAGGTGTACGCCTCTCAGCGGATGAGGGCTGGCAAGGGCAAAATGAGAAACCGCC
GGAGGACCCAGCGCAGGGGGCCCTGCGTCATCTACAACGAGGACAACGGCATCGTCAAGGCCTTCCGGAACATCCCTGGG
ATCACTCTGCTCAACGTGACCAAGCTGAACATCCTGAAGCTCGCGCCCGGTGGGCACGTGGGGCGCTTCTGCATCTGGAC
GGAGAGTGCCTTCCGGAAGCTGGACGACTTGCACGGCACTTGGCGTAAAGCCGCGTCCCTCAAGAGCGACTACAACCTTC
CCATGCACAAGATGCCCAATACAGACCTCAGCAGAATA

Alignment

ORF - retro_ocun_631 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.1 %
• Parental protein coverage: 78.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAGRRGAWLSPLPAMACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSE
          AAGRRGAWLSPLPAMACARPL.SVYSEKGESSGKNVTLPA.FKAPI.PDIVNFVHTN.RKNNRQPYAVSE
Retrocopy AAGRRGAWLSPLPAMACARPLLSVYSEKGESSGKNVTLPAMFKAPIQPDIVNFVHTNVRKNNRQPYAVSE

Parental  LAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICS
          LAGHQTSAESWGTGRAVA.IPRVRGGGTHRSGQGAF.NMCRGGRMFAPTKTW..WHRRVNTTQK.YAICS
Retrocopy LAGHQTSAESWGTGRAVAGIPRVRGGGTHRSGQGAFRNMCRGGRMFAPTKTWCHWHRRVNTTQKWYAICS

Parental  ALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKM
          ALAA.ALPALVMSKGH.IEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKM
Retrocopy ALAALALPALVMSKGHGIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYASQRMRAGKGKM

Parental  RNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGT
          RNRRR.QRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDL.GT
Retrocopy RNRRRTQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDLHGT

Parental  WRKAASLKSNYNLPMHKMLNTDLSRI
          WRKAASLKS.YNLPMHKM.NTDLSRI
Retrocopy WRKAASLKSDYNLPMHKMPNTDLSRI

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	2.21 RPM	499.23 RPM
SRP017611_kidney	2.53 RPM	744.97 RPM
SRP017611_liver	2.08 RPM	394.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_631 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_631 has 0 orthologous retrocopies within eutheria group .

---

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,