RetrogeneDB ID: retro_rnor_639

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:229798160..229798712(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000021204
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cdca5
• Ensembl ID: ENSRNOG00000046635
• Aliases: Cdca5, RGD1560863
• Description: sororin [Source:RefSeq peptide;Acc:NP_001108514]

Sequence

>retro_rnor_639
CCAGCAGCTCCAGTCAGAAAAGCCATCATCTTGAAGAAGATTGTACCTCGTGCAGTAGAGGTCCCAGATGTTCACACACC
AGTTCGCAGGAGTCCTAGGATCTCTTTTATCTTAGAAAAAGAGAACAACCCTCCGCTCAAGGTGCCCACTAAGGAGGACC
TCTTCAAGACGTGTAGCGTCCCTGGCACTCCCTCCAGCACCCCCGTGCTGTGCGCTCAGAATGTTAAGTCTAACTCTAGA
GAAGTGGAGCCGGACATCAGAGATTTGGAAATGTCTCAGAAAGTCAGGCGGTCCTACAGTCGGCTACAGAGCCTCCATTG
TGCCTCAACCTCCACCCCCGGCCGCCGATCCTTCTTTGGCTTTGAGAGACCTGAAGACTTGCCTGGAGTCTCACCTGTCG
TGCGTTCAAAGTTAATGGAGACCCCAAAGGTGCCTGTGAAACACTTGGTTCCAGATAGAACGCTCCCTGGAATCTCTCCC
CCAATTGTGAAAGAGAAACGAAAGAAGAAGGTTCCTGAGATCACGAAGTCAGAGCTGGATAAGTGGGCTGTG

Alignment

ORF - retro_rnor_639 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.65 %
• Parental protein coverage: 56.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAAPVRKAIILKKIVPRAVEVPDVHTPVRRSPRISFILEKENNPPLKVPTKEDLFKTCSVPGTPSSTPVL
          PAAPVRKAIILKKIVPRAVEVPDVHTPVRRSPRISFILEKENNPPLKVPTKEDLFKTCSVPGTPSSTPVL
Retrocopy PAAPVRKAIILKKIVPRAVEVPDVHTPVRRSPRISFILEKENNPPLKVPTKEDLFKTCSVPGTPSSTPVL

Parental  CAQNVKSNSREVEPDTRDLEMSQKVRRSYSRLQSLHCASTSTPGRRSFFGFERPEDLPGVSPVIRSKLME
          CAQNVKSNSREVEPD.RDLEMSQKVRRSYSRLQSLHCASTSTPGRRSFFGFERPEDLPGVSPV.RSKLME
Retrocopy CAQNVKSNSREVEPDIRDLEMSQKVRRSYSRLQSLHCASTSTPGRRSFFGFERPEDLPGVSPVVRSKLME

Parental  TPKVPVKHLVPDRTLPGISPPIVKEKRKKKVPEITSSTAKKIAL
          TPKVPVKHLVPDRTLPGISPPIVKEKRKKKVPEIT.S...K.A.
Retrocopy TPKVPVKHLVPDRTLPGISPPIVKEKRKKKVPEITKSELDKWAV

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	0.22 RPM
SRP017611_kidney	0.00 RPM	0.14 RPM
SRP017611_liver	0.07 RPM	0.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_639 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002502	1 retrocopy	retro_cjac_4145,
Dasypus novemcinctus	ENSDNOG00000019033	1 retrocopy	retro_dnov_2601,
Felis catus	ENSFCAG00000028197	1 retrocopy	retro_fcat_761,
Pteropus vampyrus	ENSPVAG00000007908	1 retrocopy	retro_pvam_567,
Rattus norvegicus	ENSRNOG00000046635	2 retrocopies	retro_rnor_639 , retro_rnor_640,