RetrogeneDB ID: retro_rnor_577

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:45263416..45264193(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004144
• 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_577
ATGGGATGCCGGTCTTCAGACACTGAAGAAGAAAGCAGAAGCAAGAGAAAAAAGAAACATCGGAGGCGGTCATCTTCAAG
CAGCTCTTCAGACAGCAGGACGTACAGCCGCAAGAAGGGCGGGAGGAGGCCAAGGTCGGAGTCACGATCCTGGTCTAGAG
ACCGCCAGCCTTGCTCACATTCTTATGAGAGGAGACGCAGGCGCAGGTCAAGCAGCAGCTCTTCTTATGGCTCCAGAAGA
AAAAGAAGTCGCAGTCGTTCCACGGGCCAAGGGAAATCCTATAGAGTTCAGAGGTCTCGGTCAAAAAGCAGAACAAGAAG
GTCCAGGCCAAGACCTCGTCCACGCTCACATAGTAGAAGCAGTGAAAGATCCAGTCACAGAAGAACTCGTAGAAGGTCCA
GGGACAGAGACAGACGTAAAGTTCGGGACAAAGAGAAGAGAGAAAAGGAGAAGGATAAAGGCAAAGACAAAGAGGCGCAC
AGCATCAAACGAGGGGATTGTGGAAACATCAAAGCCGGATTAGAACATCTGCCTCCAGCTGAGCAGGCCAAAGCCAGACT
TCAGTTGGTCCTTGAAGCTGCTGCAAAAGCTAATGAAGCATTAAAAGCCAAAGAAAGGAATGAGGAAGAAGCAAAGAGAA
GAAAAGAAGAAGACCGAGCCACCCTGGTAGAACAAGTAAAAAGAGTAAACGAAATTGAAGCAATTGAAAATGATTCTTTT
GTTCAGCAGACATTCAGATCAAGTAAAGATGTCAAAAAGTCGGTAGAGTCAAGTGAA

Alignment

ORF - retro_rnor_577 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRSSDTEEESRSKRKKKHRRRSSSSSSSDSRTYSRKKGGRRPRSESRSWSRDRQPRSHSYERRRRRRS
          MG.RSSDTEEESRSKRKKKHRRRSSSSSSSDSRTYSRKKGGRRPRSESRSWSRDRQP.SHSYERRRRRRS
Retrocopy MGCRSSDTEEESRSKRKKKHRRRSSSSSSSDSRTYSRKKGGRRPRSESRSWSRDRQPCSHSYERRRRRRS

Parental  SSSSSYGSRRKRSRSRSRGRGKSYRVQRSRSKSRTRRSRSRPRPRSHSRSSERSSHRRTRSRSRDRDRRK
          SSSSSYGSRRKRSRSRS.G.GKSYRVQRSRSKSRTRRSR.RPRPRSHSRSSERSSHRRTR.RSRDRDRRK
Retrocopy SSSSSYGSRRKRSRSRSTGQGKSYRVQRSRSKSRTRRSRPRPRPRSHSRSSERSSHRRTRRRSRDRDRRK

Parental  VRDKEKREKEKDKGKDKEAHTIKRGDCGNIKAGLEHLPPAEQAKARLQLVLEAAAKADEALKAKERNEEE
          VRDKEKREKEKDKGKDKEAH.IKRGDCGNIKAGLEHLPPAEQAKARLQLVLEAAAKA.EA..........
Retrocopy VRDKEKREKEKDKGKDKEAHSIKRGDCGNIKAGLEHLPPAEQAKARLQLVLEAAAKANEAXXXXXXXXXX

Parental  AKRRKEEDQATLGEQVKRVKEIEAIESDSFVQQTFRSSKDVKKSVEPSE
          .........ATL.EQVKRV.EIEAIE.DSFVQQTFRSSKDVKKSVE.SE
Retrocopy XXXXXXXXRATLVEQVKRVNEIEAIENDSFVQQTFRSSKDVKKSVESSE

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	0.14 RPM	13.59 RPM
SRP017611_kidney	0.28 RPM	8.09 RPM
SRP017611_liver	0.07 RPM	3.23 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_577 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_577 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,