RetrogeneDB ID: retro_rnor_1443

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:24083374..24084208(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000013826
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1443
ATGGCTGCCGATGGTCCTTGTGCGCTGGTCACCGGCTGCTCCGCCACCTTCACCGGGGACCGGCTGGTGCAACATATCCT
TGGAACAGAAGATGCTGTTGCGGAAGCGACTTCCAGCGATGCTGTGAGGTTTTACCCCTGGACCATCGATAACAAGTACT
ACTCTGCAGAGGTCAACCTGTGTGTGGTGCCAAGCAAGTGCCTGGTCACTGCCGAGGTCGCAGAGGCAGTCCAGGCGTTT
GTAGTTTACTTTGATAGCACACAGAAATCAGGTCTTGACAGCGTCTCCTCATGGCTTCCTCTGGCAGAAACATGGCTTCC
TGAGGTGATGATCCTGGTCTGTGATAGAGTGTGTGAAAATGGAATAAACCAACAACAGGCTCAAGAGTGGTGCATCAAAC
ATGGCTTTGAGCTGGTGGAGCTCTGCCCAGAGGAGCTACCTGAGGAGGACGATGACTTCCCTGAATCTACAGGCGTAAAG
CGGATTGTACAAGCATTGAATGCCAATGTCTGGTCCAATGCCGTGATGAAGAATGACAGGAGCCAGGGCTTCGGCCTTCT
CAGCTCACTGGCTGGAGCAAGCCGCAGTGTTGGATCAGCAGAGAGCTGTCACTGTGAGCAGGAGCCATCGCCAACAACTG
AGAGGACAGAGTCCCTCCCCGGGCATCGCAGTGGCGCGTGTGGTTCAGCAGGTGCATGGGTTGACAGCATTGTTGACCCC
ATGTTAGACCTGGATATTCAAGAATTAGCCAGTCTTACCACCGGAGGAGGGGATCTGGAGAACTTTGAGAGACTCTTTTC
AAAGTTAAAAGAAATGAAAGACAAGGCTGCTTCC

Alignment

ORF - retro_rnor_1443 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.24 %
• Parental protein coverage: 88.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAGVPCALVTSCSATFTGDRLVQHILGTEDAVVEATSSDAVRFYPWTIDNKYYSAEVNLCVVPSKCRVT
          MAA..PCALVT.CSATFTGDRLVQHILGTEDAV.EATSSDAVRFYPWTIDNKYYSAEVNLCVVPSKC.VT
Retrocopy MAADGPCALVTGCSATFTGDRLVQHILGTEDAVAEATSSDAVRFYPWTIDNKYYSAEVNLCVVPSKCLVT

Parental  AEIAEAVQAFVVYFDSTQKSGLDSVSSWLPLAETWLPEVMILVCDRVCEDGINRQQAQEWCIKHGFELVE
          AE.AEAVQAFVVYFDSTQKSGLDSVSSWLPLAETWLPEVMILVCDRVCE.GIN.QQAQEWCIKHGFELVE
Retrocopy AEVAEAVQAFVVYFDSTQKSGLDSVSSWLPLAETWLPEVMILVCDRVCENGINQQQAQEWCIKHGFELVE

Parental  LCPEELPEEDDDFPESTGVKRIVQALNANVWSNVVMKNDRSQGFSLLNSLAGASRSVGSAESCQCEQEPS
          LCPEELPEEDDDFPESTGVKRIVQALNANVWSN.VMKNDRSQGF.LL.SLAGASRSVGSAESC.CEQEPS
Retrocopy LCPEELPEEDDDFPESTGVKRIVQALNANVWSNAVMKNDRSQGFGLLSSLAGASRSVGSAESCHCEQEPS

Parental  PTAERTESLPGHRSGACGPAGAQVDSIVDPMLDLDIQELASLTTGGGDLENFERLFSKLKEMKDKAAT
          PT.ERTESLPGHRSGACG.AGA.VDSIVDPMLDLDIQELASLTTGGGDLENFERLFSKLKEMKDKAA.
Retrocopy PTTERTESLPGHRSGACGSAGAWVDSIVDPMLDLDIQELASLTTGGGDLENFERLFSKLKEMKDKAAS

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_1443 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1443 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,