RetrogeneDB ID: retro_rnor_2317

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:111815125..111816049(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004582
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Taf8
• Ensembl ID: ENSRNOG00000015249
• Aliases: Taf8, Tbn
• Description: transcription initiation factor TFIID subunit 8 [Source:RefSeq peptide;Acc:NP_001101667]

Sequence

>retro_rnor_2317
ATGGCTGACCCGGCGGCCCGGCCTGGTGGCTCCAGAACGAGAGCAGGAAATAAACAGTCCACTAACCCTGCTGATAACTA
CCACCTGGCCCGCAGGAGGACCCTGCAAGTGGTTGTGAGCTCTTTGCTGACAGAGGCGGGATTTGAGAGCGCGGAGAAAG
CGTCTGTGGAGACGTTGACAGAGATGTTACAGAGCTACCTCTCAGAAATAGGGAGAAGCGCCAAGTCATACTGCGAGCAC
ACAGCCAGGACCCAGCCCACACTTTCAGACATCGTGGTCACACTGGTTGAAATGGGGTTCAATGTTGGCATTCTACCTGC
TTATGCAAAACGGTCTCAGAGGATGGTCATCACTGCACCTCCGGTGACCAATCAGCCAGTGACACCCAAGGCCCTCACTG
CAGGGCAGAACCGACCCCACCCGCCACACATCCCCAGCCATTTTCCTGAATTTCCGGATCCCCACACGTACATCAAAACA
CCGACGTACCGCGAGCCAGTGTCTGACTACCAGGTCCTCCGAGAGAAGGCCTCATCTCAGAGGCGGGACGTGGAGCGAGC
ACTCACCCGCTTCTTGGCCAAGACAGGCGAGACCCAGAATCTCTTCAAGGATGATGTCAGCACTTTTCCCTTGATTGCAG
CCAGATCTTTCACCATCCCCTACCTCACGGCCTTGCTTCCCTCTGAGCTGGAGATACAGCAGATGGAAGAGATGGACTCC
TTGGAGCAGGACGAGCAAACAGATACAGAGAACATCGCGCTTCATATCAGCTCGGACGAATCCGGAGCTGAGAAGGAGAA
TACTTCTGTCCTGCAGCAGAACTCCTCCTTGTCCGGCAGCCGGAACGGGGAGGAGAACATCATCGATAACCCCTATCTGC
GGCCCGTGAAGAGGCCCAAGATCTGGAGGAAGAAGTCCCTCTCG

Alignment

ORF - retro_rnor_2317 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADTATGPGGSGTRPGNKQSTNPADNYHLARRRTLQVVVSSLLTEAGFESAEKASVETLTEMLQSYISEI
          MAD.A..PGGS.TR.GNKQSTNPADNYHLARRRTLQVVVSSLLTEAGFESAEKASVETLTEMLQSY.SEI
Retrocopy MADPAARPGGSRTRAGNKQSTNPADNYHLARRRTLQVVVSSLLTEAGFESAEKASVETLTEMLQSYLSEI

Parental  GRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVDTLPAYAKRSQRMVITAPPVTNQPVTPKALTAGQNRPH
          GRSAKSYCEHTARTQPTLSDIVVTLVEMGFNV..LPAYAKRSQRMVITAPPVTNQPVTPKALTAGQNRPH
Retrocopy GRSAKSYCEHTARTQPTLSDIVVTLVEMGFNVGILPAYAKRSQRMVITAPPVTNQPVTPKALTAGQNRPH

Parental  PPHIPSHFPEFPDPHTYIKTPTYREPVSDYQVLREKAASQRRDVERALTRFMAKTGETQSLFKDDVSTFP
          PPHIPSHFPEFPDPHTYIKTPTYREPVSDYQVLREKA.SQRRDVERALTRF.AKTGETQ.LFKDDVSTFP
Retrocopy PPHIPSHFPEFPDPHTYIKTPTYREPVSDYQVLREKASSQRRDVERALTRFLAKTGETQNLFKDDVSTFP

Parental  LIAARPFTIPYLTALLPSELEIQQMEETDSSEQDEQTDTENIALHISTDESGAEKENTSVLQQNSSLSGS
          LIAAR.FTIPYLTALLPSELEIQQMEE.DS.EQDEQTDTENIALHIS.DESGAEKENTSVLQQNSSLSGS
Retrocopy LIAARSFTIPYLTALLPSELEIQQMEEMDSLEQDEQTDTENIALHISSDESGAEKENTSVLQQNSSLSGS

Parental  RNGEESTIDNPYLRPVKKPKIRRKKSLS
          RNGEE..IDNPYLRPVK.PKI.RKKSLS
Retrocopy RNGEENIIDNPYLRPVKRPKIWRKKSLS

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	17.83 RPM
SRP017611_kidney	0.00 RPM	17.86 RPM
SRP017611_liver	0.00 RPM	9.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2317 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2317 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010516	1 retrocopy	retro_chof_661,
Macropus eugenii	ENSMEUG00000006952	1 retrocopy	retro_meug_150,
Microcebus murinus	ENSMICG00000011353	6 retrocopies	retro_mmur_112, retro_mmur_1455, retro_mmur_443, retro_mmur_455, retro_mmur_554, retro_mmur_555,
Monodelphis domestica	ENSMODG00000012785	2 retrocopies	retro_mdom_1206, retro_mdom_1357,
Mus musculus	ENSMUSG00000023980	1 retrocopy	retro_mmus_436,
Otolemur garnettii	ENSOGAG00000016885	1 retrocopy	retro_ogar_759,
Rattus norvegicus	ENSRNOG00000015249	1 retrocopy	retro_rnor_2317 ,