RetrogeneDB ID: retro_rnor_2454

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:43631657..43632241(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000023762
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rsrc1
• Ensembl ID: ENSRNOG00000012639
• Aliases: None
• Description: serine/Arginine-related protein 53 [Source:RefSeq peptide;Acc:NP_001014194]

Sequence

>retro_rnor_2454
ATGGGACACCGGTCTTCAAACACTGAAGACGAAAGAAGAAGCAAGAGGAAAAAGAAACACTGGAGGCGGTCATCTTCAAA
CAGCTCTTCAAACAGCAGGACATATAGTAGCAAGAAGGGCGGGAGGAGGCCAAGGTCGGAGTCAGGATCCTGGTATAGAG
ACGGCCAGCCTAGCTCACATTCTCATGAGAGAAGACGCAGGCGCAGGTCAAGCAGCAGCTCTTCTTATGGCTCCAGAAGA
CAAAGAAGTCGCAGTCGCTCCAGGGGCCGAGGGAAAGCCTATAGAGTAAAGAGGTCTCGGCCAAAAAGCAGAACAAGAAG
GTCCAGGTCAAGACCTCGTTCACGCTCGCATAGTAGAAGCAGTGAAAGAACCAGCCACAGAAGAACTCGTAGTAGGTCCA
GGGATAGAGACAGACGTAAAGGGACAAAAAGAGGAGAGAAAAGGAGAAGGATAAAGGCAAAGACAAAGAGGTGTACAGCA
TCAAATGCCAGGATTGTGGAAACATCAAGGCTGGATTAGAACATCTGCCTCCAGCTGAGCAGGCCAAAGCCAGACTTCAC
TTGGTCCTTGAAGCTGCTGCAAAA

Alignment

ORF - retro_rnor_2454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.83 %
• Parental protein coverage: 58.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSDSRTYSRKKGGRRPRSESRSWSRDRQPRSHSYERRRRRRS
          MG.RSS.TE.E.RSKRKKKH.RRSSS.SSS.SRTYS.KKGGRRPRSES.SW.RD.QP.SHS.ERRRRRRS
Retrocopy MGHRSSNTEDERRSKRKKKHWRRSSSNSSSNSRTYSSKKGGRRPRSESGSWYRDGQPSSHSHERRRRRRS

Parental  SSSSSYGSRRKRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRDRDRRK
          SSSSSYGSRR.RSRSRSRGRGK.YRV.RSR.KSRTRRSRSRPR.RSHSRSSER.SHRRTRSRSRDRDRRK
Retrocopy SSSSSYGSRRQRSRSRSRGRGKAYRVKRSRPKSRTRRSRSRPRSRSHSRSSERTSHRRTRSRSRDRDRRK

Parental  -VRDKEKR-EKEKDKGKDKEAHTIKRGDCGNIKAGLEHLPPAEQAKARLQLVLEAAAK
          .....EKR.EK...KGKDKE...IK..DCGNIKAGLEHLPPAEQAKARL.LVLEAAAK
Retrocopy GTKRGEKR<EKD--KGKDKEVYSIKCQDCGNIKAGLEHLPPAEQAKARLHLVLEAAAK

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	13.59 RPM
SRP017611_kidney	0.00 RPM	8.09 RPM
SRP017611_liver	0.00 RPM	3.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2454 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2454 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004797	1 retrocopy	retro_cjac_553,
Cavia porcellus	ENSCPOG00000000876	2 retrocopies	retro_cpor_618, retro_cpor_671,
Echinops telfairi	ENSETEG00000017217	1 retrocopy	retro_etel_1555,
Homo sapiens	ENSG00000174891	1 retrocopy	retro_hsap_4281,
Mus musculus	ENSMUSG00000034544	1 retrocopy	retro_mmus_666,
Nomascus leucogenys	ENSNLEG00000004137	1 retrocopy	retro_nleu_2851,
Rattus norvegicus	ENSRNOG00000012639	2 retrocopies	retro_rnor_2454 , retro_rnor_577,
Tupaia belangeri	ENSTBEG00000001973	13 retrocopies	retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840,