RetrogeneDB ID: retro_rnor_2813

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:68262090..68263003(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aagab
• Ensembl ID: ENSRNOG00000008424
• Aliases: Aagab, P34
• Description: Alpha- and gamma-adaptin-binding protein p34 [Source:UniProtKB/Swiss-Prot;Acc:Q9R0Z7]

Sequence

>retro_rnor_2813
GCTGTTTGTGTCCCCTGTGAGCTGGTCACCAGCTGCTCCGCCACCTTCACCGGGGACTGGCTGGTGCAACATATTCTTGG
AACAGAAGATGCTGTTGTGGAAGGGACTTCCAGCGATGCTGTGAGGTTTTACCCCTGGACCATCAATAACAAGTACTATT
CTGCAGAGATCAACCTGTGTGTGGTGCCAGGCAAGTGAGTGGTCACTGCCAAGATCTCAGAGTCAGTCCAGGCATTTGTT
TTTTTACTTTGACAGCACATAGAAATCAGGTCTTGACACCATCTCCTCATGGCTTCCTCTGGCAGAAACATGGCTGCCTG
AGGTGACGATCCTGGTCTGTGATAGAGTGTATGGAGATGGAATAAACTGGCAACAGGCTCAGCATCAAACGTGGTGCATC
AAACGTGGCTTTGAGCTGGTGGAGGAGCTGCCCAAGGAGGACGATGACTTCCCTGAATCTACAGGCATAAAGTGGATTGT
ACAAGCATTGAATGCCAATGTCTGATCTAATGTCGTGATGAAGAATGACAGGAGCCAGGACTTCAGCCTTCTCAACTCAC
TGGCTGGAGCAAGCCACAGAGTTGGATCAGCAGAGAATTGTCACTGTGAGCAGCCAACATCTGAGAGGACAGAGTTCCTT
CTGGAGCATCATAGTGGTGCGTGTGGCTCAGCAGGTACACAGGTTGGCAGCATTGTCAATCCCATGTTAGACCTGGGTAT
TCGACAATTAGCCAGTCTGGGGTGGGAACTGGAGAACTTTGAGAGACTCTTTTCAAAGTTAAAAGAAATGAAAGACAAGG
CTGCAACACTTCCTCATGAGCAAAGAAAGTTGCATGCAGAAAAGGTTGCCAAAGCCTTCTGGATGGCAATAGGGGAAGAC
CGAGATGAGATTGAGGACCTTTCTTATGATGAG

Alignment

ORF - retro_rnor_2813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 99.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAGVPCALVTSCSATFTGDRLVQHILGTEDAVVEATSSDAVRFYPWTIDNKYYSAEVNLCVVPSKCRVTA
          A..VPC.LVTSCSATFTGD.LVQHILGTEDAVVE.TSSDAVRFYPWTI.NKYYSAE.NLCVVP.K..VTA
Retrocopy AVCVPCELVTSCSATFTGDWLVQHILGTEDAVVEGTSSDAVRFYPWTINNKYYSAEINLCVVPGK*VVTA

Parental  EIAEAVQAFV-VYFDSTQKSGLDSVSSWLPLAETWLPEVMILVCDRVCEDGINRQQAQE--WCIKHGFEL
          .I.E.VQAFV..YFDST.KSGLD..SSWLPLAETWLPEV.ILVCDRV..DGIN.QQAQ...WCIK.GFEL
Retrocopy KISESVQAFV>FYFDST*KSGLDTISSWLPLAETWLPEVTILVCDRVYGDGINWQQAQHQTWCIKRGFEL

Parental  VELCPEELPEEDDDFPESTGVKRIVQALNANVWSNVVMKNDRSQGFSLLNSLAGASRSVGSAESCQCEQE
          VE....ELP.EDDDFPESTG.K.IVQALNANV.SNVVMKNDRSQ.FSLLNSLAGAS..VGSAE.C.CEQ.
Retrocopy VE----ELPKEDDDFPESTGIKWIVQALNANV*SNVVMKNDRSQDFSLLNSLAGASHRVGSAENCHCEQ-

Parental  PSPTAERTESLPGHRSGACGPAGAQVDSIVDPMLDLDIQELASLTTGGGDLENFERLFSKLKEMKDKAAT
          ..PT.ERTE.L..H.SGACG.AG.QV.SIV.PMLDL.I..LASL...G..LENFERLFSKLKEMKDKAAT
Retrocopy --PTSERTEFLLEHHSGACGSAGTQVGSIVNPMLDLGIRQLASL---GWELENFERLFSKLKEMKDKAAT

Parental  LPHEQRKLHAEKVAKAFWMAIGGDRDEIEGLSSDD
          LPHEQRKLHAEKVAKAFWMAIG.DRDEIE.LS.D.
Retrocopy LPHEQRKLHAEKVAKAFWMAIGEDRDEIEDLSYDE

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	30.77 RPM
SRP017611_kidney	0.00 RPM	20.31 RPM
SRP017611_liver	0.00 RPM	5.72 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2813 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2813 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2813 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000040368	1 retrocopy	retro_btau_723,
Canis familiaris	ENSCAFG00000017414	1 retrocopy	retro_cfam_1891,
Monodelphis domestica	ENSMODG00000009585	1 retrocopy	retro_mdom_1416,
Rattus norvegicus	ENSRNOG00000008424	2 retrocopies	retro_rnor_1443, retro_rnor_2813 ,