RetrogeneDB ID: retro_rnor_294

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:200757116..200757491(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000048424
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Paip2
• Ensembl ID: ENSRNOG00000019934
• Aliases: None
• Description: Polyadenylate-binding protein-interacting protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q6AXZ0]

Sequence

>retro_rnor_294
ATGAAAGATCCAAGTCGCAGCAGTACGAGCCCAAGCATCATCAATGACGATGTGATTATTAATGGTCATTCTCATGAAGA
GGATAATCCATTTGCAGAGTACATGTGGACGGAAAATGAAGAGGAATTCAACAGACAAATAGAAGAGGAGTTGTGGGAAG
AAGAATTTATTGAACACTGTTTCCAAGAAATGCTGGAAGAGGAAGAAGAACATGAATGGTTTATTCCAGCCCGAGCTCTC
CCACAAACTATGGACCAAATCCAAGACCAGTTTAATGACCTTGTTATCAGTGATGGCTCTTCTCTGGAAGATTTTGTGCT
GACGAGCAATCTGAATCCCAATGCAAAGGAGTTTGTTCCTGGGGTGAAGTACTGA

Alignment

ORF - retro_rnor_294 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDPSRSSTSPSIINDDVIINGHSHEEDNPFAEYMWMENEEEFNRQIEEELWEEEFIERCFQEMLEEEEE
          MKDPSRSSTSPSIINDDVIINGHSHEEDNPFAEYMW.ENEEEFNRQIEEELWEEEFIE.CFQEMLEEEEE
Retrocopy MKDPSRSSTSPSIINDDVIINGHSHEEDNPFAEYMWTENEEEFNRQIEEELWEEEFIEHCFQEMLEEEEE

Parental  HEWFIPARDLPQTMDQIQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY
          HEWFIPAR.LPQTMDQIQDQFNDLVISDGSSLED.V..SNLNPNAKEFVPGVKY
Retrocopy HEWFIPARALPQTMDQIQDQFNDLVISDGSSLEDFVLTSNLNPNAKEFVPGVKY

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	57.73 RPM
SRP017611_kidney	0.00 RPM	73.27 RPM
SRP017611_liver	0.00 RPM	28.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_294 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_294 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006982	1 retrocopy	retro_cjac_212,
Dipodomys ordii	ENSDORG00000002264	1 retrocopy	retro_dord_676,
Microcebus murinus	ENSMICG00000012451	1 retrocopy	retro_mmur_1085,
Rattus norvegicus	ENSRNOG00000019934	1 retrocopy	retro_rnor_294 ,
Tupaia belangeri	ENSTBEG00000004105	1 retrocopy	retro_tbel_1370,