RetrogeneDB ID: retro_rnor_709

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:73799138..73799759(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000027511
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Taf11
• Ensembl ID: ENSRNOG00000024601
• Aliases: None
• Description: Transcription initiation factor TFIID subunit 11 [Source:UniProtKB/Swiss-Prot;Acc:Q5U1X0]

Sequence

>retro_rnor_709
ATGGAAAACCTTGGAGAGTCGCCCACGGACAAAGGCGGGGAGTCAGAGGAGTCGAGGGCTACTCCTGGGAACCCGTTAGC
GGCAGACACTGAGGGAATCCCTGAGGAAACCGATAGGGATGGAGACGTGGACTTGAAAGAAGCCGCGGCAGAGGAAAGGG
AGACCAAGAGTCAGGATGTCTCAGGTTTGACAGCAGTTGAGAGGGAAGACTCATTTCTTACTCCTGCAGCCAAAAAGCTG
AAACTAGAAACCAAAGACAAGAAGGAGAAGAAGCAGAAGGTGGACGAAGATGAGATTCAGAAGATGCAAATCCTGGTCTC
TTCTTTTTCTGAAGAGCAGCTGAACCGTTATGAAATGTATCGCCGGTCAGCTTTCCCGAAGGCAGCCATTAAAAGGCTGA
TCCAGTCCATCACTGGCACCTCTGTGTCTCAGAATGTTGTGATCGCCATGTCTGGCATTTCTAAAGTTTTTGTCGGGGAG
GTGGTAGAAGAAGCCCTGGATGTGTGTGAGAAATGGGGAGAAATGCCACCCCTGCAGCCCAAGCACATGAGGGAGGCCGT
GCGGAGGTTGAAGTCCAAGGGGCAAATCCCCAGCTCAAAGCACAAGAAAATCACCTTCTTC

Alignment

ORF - retro_rnor_709 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDNLGESPTDKAGEPGESEETRATPGAPVSADTEGIPEETDQVGDADSKEAAAEESELKSQDVSDVTAAE
          M.NLGESPTDK....GESEE.RATPG.P..ADTEGIPEETD..GD.D.KEAAAEE.E.KSQDVS..TA.E
Retrocopy MENLGESPTDKG---GESEESRATPGNPLAADTEGIPEETDRDGDVDLKEAAAEERETKSQDVSGLTAVE

Parental  REDPSLLTPAAKKLKLDTKDKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS
          RED.S.LTPAAKKLKL.TKDKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS
Retrocopy RED-SFLTPAAKKLKLETKDKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS

Parental  ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPNSKHKKITF
          ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIP.SKHKKITF
Retrocopy ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPSSKHKKITF

Parental  F
          F
Retrocopy F

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	1.08 RPM	9.99 RPM
SRP017611_kidney	3.77 RPM	12.49 RPM
SRP017611_liver	1.82 RPM	5.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_709 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015428	1 retrocopy	retro_cpor_629,
Loxodonta africana	ENSLAFG00000011482	1 retrocopy	retro_lafr_1108,
Oryctolagus cuniculus	ENSOCUG00000002023	1 retrocopy	retro_ocun_447,
Rattus norvegicus	ENSRNOG00000024601	1 retrocopy	retro_rnor_709 ,