RetrogeneDB ID: retro_rnor_266

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:40106380..40106956(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000003575
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Vapa
• Ensembl ID: ENSRNOG00000014765
• Aliases: None
• Description: Vesicle-associated membrane protein-associated protein A [Source:UniProtKB/Swiss-Prot;Acc:Q9Z270]

Sequence

>retro_rnor_266
ATGGCGTCCGTCTCCCGCGCCCCCGCGAAGCCCCCGCAGATCCTAGTCCTCGACCCACCCACGGACCTCAAGTTCAAAGG
CCCCTTCACCGCGGTAGCCACGGCGCATCTTAAACTGCGCAACCCGTCGACGAGGAAAGTGTGCTTCAAGGTGAAGAGCA
CCAGCCCTCGGCGCTACTGCGTGCGGCCCAACAGCGGCGTCATCGAGCCAGGCTGCACAGTGACGGTCGCCGCCATGCTG
CAGCCCTCCTGCTGCGGCCCCAGCCAGGAGGTCAAGCACAAGTTCATGGTGCAGACAGTGTTTGCTCCTCCGGACACTTC
AGATCTGGAGGCCGTGTGGAGGGGGGTAAACCCCGGGGAATTAATGGATTCGAAATTAAGGTGTGTATTTGAAGCGCCGA
CAGAAAGTGACAAACTGGAAGATGGCTTGAGACTCAGAAAGGTAGCGCATCCTGACAAGCCAGGACCCTCCTCCTGCACG
TCCTTGAAGAAGGGTTATACCACGCCTCTTCCTGTTGTTCTGCTGGTGATCGGAGCAGTTTTCTTTGGATTCTTTCTAGG
GAAACTCGTCTTGTAG

Alignment

ORF - retro_rnor_266 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.63 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASASGAMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDP
          MAS.S.A.AK..QILVLDPP.DLKFKGPFT.V.T..LKL.NPS.RKVCFKVK.T.PRRYCVRPNSGVI.P
Retrocopy MASVSRAPAKPPQILVLDPPTDLKFKGPFTAVATAHLKLRNPSTRKVCFKVKSTSPRRYCVRPNSGVIEP

Parental  GSIVTVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEMPNENDKLN
          G..VTV..MLQP....P....KHKFMVQT.FAPP..SD.EAVW....P.ELMDSKLRCVFE.P.E.DKL.
Retrocopy GCTVTVAAMLQPSCCGPSQEVKHKFMVQTVFAPPDTSDLEAVWRGVNPGELMDSKLRCVFEAPTESDKLE

Parental  D
          D
Retrocopy D

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	127.40 RPM
SRP017611_kidney	0.07 RPM	105.30 RPM
SRP017611_liver	0.00 RPM	64.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_266 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_266 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1774

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006042	2 retrocopies	retro_cpor_783, retro_cpor_931,
Myotis lucifugus	ENSMLUG00000008965	1 retrocopy	retro_mluc_542,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57,
Mus musculus	ENSMUSG00000024091	1 retrocopy	retro_mmus_1774,
Pongo abelii	ENSPPYG00000009006	1 retrocopy	retro_pabe_1323,
Rattus norvegicus	ENSRNOG00000014765	1 retrocopy	retro_rnor_266 ,