RetrogeneDB ID: retro_rnor_443

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:64407205..64407590(+)
• Located in intron of: ENSRNOG00000027762

Retrocopy information

• Ensembl ID: ENSRNOG00000039739
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pdcd7
• Ensembl ID: ENSRNOG00000014340
• Aliases: None
• Description: programmed cell death protein 7 [Source:RefSeq peptide;Acc:NP_001102238]

Sequence

>retro_rnor_443
CTGCATCTTTGAGAGAGGGCCCTGGAAAGTGAGGTTGAGCAGAGGCAATGGCCGCGCAGGCCCTGGAACTAGAGCAGGAG
ATTGACCACTGGAGGATGAAGTGCGTGCAGGAAGTGGAGGAAAGGAAGCAGGAACAGGAACTCAAAGCAGCTGCTGATGG
GGTCTTAGCTGAAGTAAGGAAAAAGGAATCAGACACCAAAAGAATGGTGGACATTCCGCGCGCGTTGGAGAAATTGAGAA
AACTGAGAAAAGAAACTGCAGCAAGGAAAGGGGTCTGTCCTCCTGCATCAGATGAGACTTTGAGCACCATCTTCAGTGGC
TGAGAAAGCTCATTAAAAAGCGCTCTGAACTGTATGAAGCCGAAGAGAGAGCCCTCCGAGTTATG

Alignment

ORF - retro_rnor_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 51.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRLRERARERETER-EAEAAQATEREQEIDRWRMKCVQEVEEKKREQELKAAADGVLAEVRKKQSDTKRM
          L.L.ERA.E.E.E..EA.AAQA.E.EQEID.WRMKCVQEVEE.K.EQELKAAADGVLAEVRKK.SDTKRM
Retrocopy LHL*ERALESEVEQ<EAMAAQALELEQEIDHWRMKCVQEVEERKQEQELKAAADGVLAEVRKKESDTKRM

Parental  VDILRALEKLRKLRKEAAARKGVCPPAAADET-FEHHLQRLRKLIKKRSELYEAEERALRVM
          VDI.RALEKLRKLRKE.AARKGVCPP.A.DET.FEHHLQ.LRKLIKKRSELYEAEERALRVM
Retrocopy VDIPRALEKLRKLRKETAARKGVCPP-ASDET<FEHHLQWLRKLIKKRSELYEAEERALRVM

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	25.74 RPM
SRP017611_kidney	0.00 RPM	40.96 RPM
SRP017611_liver	0.07 RPM	14.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_443 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_443 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032076	1 retrocopy	retro_cfam_2181,
Choloepus hoffmanni	ENSCHOG00000007218	1 retrocopy	retro_chof_1625,
Rattus norvegicus	ENSRNOG00000014340	1 retrocopy	retro_rnor_443 ,