RetrogeneDB ID: retro_rnor_909

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:38446373..38447354(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tcf4
• Ensembl ID: ENSRNOG00000012405
• Aliases: None
• Description: transcription factor 4 [Source:RefSeq peptide;Acc:NP_445821]

Sequence

>retro_rnor_909
AAAGTCAGAAAAGATCCTCCAGGTTTGCAGTCTTCAGTCTATGTTTCTTCAGCCAAAACTGCCAACTACAACAGTGACTC
ACCAGGCTATTCTTCTTGCAAGACAGCAGCCAGCACTTTCTTTAGCTTCTTCTTCATGCAAGATGGCCATCACAGCAGTG
ACCCTAGGAGCTCCTCCAGTGGAATGAATCAGTCTGGCTATGGAGGCATGCTAGGCAATTCTCATATTCCACAGTCTAGC
AGCTACTGTAGCCTGCATCCAAATGATCATTTGAGCTACCTATCACACTCCTCGGCAGACATCATCTCCAGTTTTCCTCC
GATGTCTACATTCTATCTAACTGGCACAAACCATTACAGCACCTCTTCCTGCACACCTCCTGCCAATGGAACAGACGGTA
TAAAGGCAAACAGAGGAAGTGAGGCAGGAGGCAGCTCCCAGACTGGAGACCCTCTGGGGAAAGACCTGGCTTCGATCTAT
TCTCCTGATCACAAGAACAACAGCTTTTCCTCAAACATTTCAACTCATGTTGGCTCCCCTCCTTCACTCTCAGCAGGCAC
AGCTGTTTGGTCTTGAAACAGAGTACAGGCCTGGTCATCTCCCAATTACAAAGGACACTTGCACTCCTTGCAAAGCCAAA
TTGAAGACCATTGAGAAAGACTGGATGATGCAATCAATTCATGTTCTCGGGAATCACATAGTGGGCCCGTCCACAGCTGT
GCCTGGTGGTCATGGGGACATACATGGGATTATTGGACCCTCTCACAATGGAGCAATGGGTAGTCTGGGCTCAGGGTACG
GAACTCTCCTTTTCTCAGCCAACAGACATTCACTCATGATTGGGGTCCACGGTGAAGATGGCGTGGCACCAAGAGGCAGA
CATTCTCTCCTGCCAAACCAGGTTCCGGTTCCACAGCTTCGGGTCCAGTCTGCAACTTTCCTTGACTCCAACCCACCCAA
GACCCTTACAGAGGGATGCCA

Alignment

ORF - retro_rnor_909 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.85 %
• Parental protein coverage: 55.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVRKVPPGLPSSVYAPSASTADYNRDSPGYSSSKPAASTFSSSFFMQDGHHSSDPWSSSSGMNQPGYGGM
          KVRK.PPGL.SSVY..SA.TA.YN.DSPGYSS.K.AASTF.S.FFMQDGHHSSDP.SSSSGMNQ.GYGGM
Retrocopy KVRKDPPGLQSSVYVSSAKTANYNSDSPGYSSCKTAASTFFSFFFMQDGHHSSDPRSSSSGMNQSGYGGM

Parental  LGNSHIPQSSSYCSLHPHERLSYPSHSSADINSSLPPMSTFHRSGTNHYSTSSCTPPANGTDSIMANRGT
          LGNSHIPQSSSYCSLHP...LSY.SHSSADI.SS.PPMSTF...GTNHYSTSSCTPPANGTD.I.ANRG.
Retrocopy LGNSHIPQSSSYCSLHPNDHLSYLSHSSADIISSFPPMSTFYLTGTNHYSTSSCTPPANGTDGIKANRGS

Parental  GAAGSSQTGDALGKALASIYSPDHTNNSFSSNPSTPVGSPPSLSAGTAVWSRNGGQASSSPNYEGPLHSL
          .A.GSSQTGD.LGK.LASIYSPDH.NNSFSSN.ST.VGSPPSLSAGTAVWS.N..QA.SSPNY.G.LHSL
Retrocopy EAGGSSQTGDPLGKDLASIYSPDHKNNSFSSNISTHVGSPPSLSAGTAVWS*NRVQAWSSPNYKGHLHSL

Parental  QSRIEDRLERLDDAIH-VLRNHAVGP-STAVPGGHGDMHGIIGPSHNGAMGSLGSGYGTGLLSANRHSLM
          QS.IED..ERLDDAI....R....GP.STAVPGGHGD.HGIIGPSHNGAMGSLGSGYGT.L.SANRHSLM
Retrocopy QSQIEDH*ERLDDAINSCSRESHSGP>STAVPGGHGDIHGIIGPSHNGAMGSLGSGYGTLLFSANRHSLM

Parental  VGAHREDGVALRGSHSLLPNQVPVPQLPVQSATSPDLNPP-QDPYRGMP
          .G.H.EDGVA.RG.HSLLPNQVPVPQL.VQSAT..D.NPP.QDPYRGMP
Retrocopy IGVHGEDGVAPRGRHSLLPNQVPVPQLRVQSATFLDSNPP<QDPYRGMP

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	72.18 RPM
SRP017611_kidney	0.00 RPM	16.47 RPM
SRP017611_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_909 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_909 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_909 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000012405	2 retrocopies	retro_rnor_909 , retro_rnor_910,