RetrogeneDB ID: retro_rnor_442

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:64369732..64370296(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psrc1
• Ensembl ID: ENSRNOG00000020013
• Aliases: None
• Description: Proline/serine-rich coiled-coil protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3KR66]

Sequence

>retro_rnor_442
CCTACCTCCAACCAACCTGAGTTCCGGAGCAGTGATAAAAAGGGGTCAGCCAGAGCTGTTCTGGTGGCAGCTGGAAAGAA
GCCTCCAGCATAAAGAAGGAATCACCCACTTGCAATCTGTTCTCTGCATCCAAAATCCCAGGGCGCTCTCCTCTTGCAAA
CCGACTCTTCCACCTCGGAAGAAAACTGGGTCCGGCACACAGACAACAGCAAGCCTGCCAATCCCTGTCAGACCAGCTCC
ACAGGCCTCAGCTAGCAGTTCCCAGTGTTCACCCTCACTATAGGGAGCAGCCGCCAAGTGTTCTAGTCACCCATTCTCTC
AGCCATCCTCAAGCCTGTCACCCGAATGCCACTCACTGGGTGGGGTATACCACCTGGCAAAGGTGCCCTGGCTCCAGATC
CTCTCTCATCTCAGAAAGGGCAACCAAGTGCCATAGGGCACAGAGCTCCTGTTTCCCAGCAAACAAATCTTCCAACCACC
AGTGCTGGTTGAGGCAGGACCTCCAGTGCTGCTCCGGGCAGGATGCAGCCCCTCAGGAAAGCTGCAGTCCCTGGACCTAC
TAGA

Alignment

ORF - retro_rnor_442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.98 %
• Parental protein coverage: 57.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PPSNLTGLRSSDKKGSARAGRVTAGKKP-SSIKKESPTCNLFSASKNPGRSPLA-QPTLPPRRKTGSGAR
          P.SN....RSSDKKGSARA..V.AGKKP.SSIKKESPTCNLFSASK.PGRSPLA..PTLPPR.KTGSG..
Retrocopy PTSNQPEFRSSDKKGSARAVLVAAGKKP<SSIKKESPTCNLFSASKIPGRSPLA<KPTLPPRKKTGSGTQ

Parental  TVASPPIPVRPAPQSSASNSQCSSWLQGAAAKSSSRLPFP-SAIPKPAIRMPLTGRSIPAGKGALAPDPL
          T.AS.PIPVRPAPQ.SAS.SQCS..L.GAAAK.SS..PF..SAI.KP..RMPLTG..IP.GKGALAPDPL
Retrocopy TTASLPIPVRPAPQASASSSQCSPSL*GAAAKCSSH-PFS<SAILKPVTRMPLTGWGIPPGKGALAPDPL

Parental  PTQKGHPSTVGHRAPVSQRTNLPTIGAARGRTSSAARGRVQPLRKAAVPGPTR
          ..QKG.PS..GHRAPVSQ.TNLP.................QPLRKAAVPGPTR
Retrocopy SSQKGQPSAIGHRAPVSQQTNLPXXXXXXXXXXXXXXXXXQPLRKAAVPGPTR

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	0.29 RPM	7.19 RPM
SRP017611_kidney	0.70 RPM	0.42 RPM
SRP017611_liver	0.61 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_442 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_442 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000001045	1 retrocopy	retro_ptro_3012,
Rattus norvegicus	ENSRNOG00000020013	1 retrocopy	retro_rnor_442 ,