RetrogeneDB ID: retro_rnor_2840

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:106348342..106348685(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000043424
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pdcd6
• Ensembl ID: ENSRNOG00000014485
• Aliases: None
• Description: programmed cell death protein 6 [Source:RefSeq peptide;Acc:NP_001100922]

Sequence

>retro_rnor_2840
CTGTTTGACCTAGAAAACAAGGCTGGTGTGAACTTCAAGGAATTCACAGGTGTGTGGAAGCATTTCACAGACTGGCAGAA
TGTCTTCCAGACCTGTGACAGGGACAACTCGGGGATGATTGACAAAAACAAGTTCAAACAAGAACTCTCAGGCTACCGGC
TCTCTGATCAGTTCCATGACACCCTCATCCGAAAATCTGACAGGCCAAGGAAGAGGGCAGATCACATTTGATGACTTCAT
CCAGGGTTGCGTTTTCTTGCAGAAGTTGATAGACATATTCAGACGCTATGACAGGGATCAGGACAACTGGATTCAAGTAT
CTTATGAGCAGTATCTCTCCATG

Alignment

ORF - retro_rnor_2840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 60.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKHELKQALSGFGYRLSDQFHDILIRKFDR
          .FD.ENKAGVNF.EFTGVWK..TDWQNVF.T.DRDNSGMIDK...KQ.LS..GYRLSDQFHD.LIRK.DR
Retrocopy LFDLENKAGVNFKEFTGVWKHFTDWQNVFQTCDRDNSGMIDKNKFKQELS--GYRLSDQFHDTLIRKSDR

Parental  -QGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSM
          .QGRGQI.FDDFIQGC..LQ.L.DIFRRYD.DQD.WIQVSYEQYLSM
Retrocopy >QGRGQITFDDFIQGCVFLQKLIDIFRRYDRDQDNWIQVSYEQYLSM

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	30.27 RPM
SRP017611_kidney	0.00 RPM	43.96 RPM
SRP017611_liver	0.00 RPM	19.57 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2840 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2840 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008464	1 retrocopy	retro_amel_498,
Canis familiaris	ENSCAFG00000011044	2 retrocopies	retro_cfam_1289, retro_cfam_1695,
Felis catus	ENSFCAG00000025521	1 retrocopy	retro_fcat_1800,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,
Rattus norvegicus	ENSRNOG00000014485	1 retrocopy	retro_rnor_2840 ,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,