RetrogeneDB ID: retro_rnor_1601

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:8705573..8706194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ubxn1
• Ensembl ID: ENSRNOG00000019666
• Aliases: Ubxn1, 2B28, RGD1309471
• Description: UBX domain-containing protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q499N6]

Sequence

>retro_rnor_1601
AGAGGAGAACAGACTGAGAGAATGTTGGGAATTGTGTCACAGAAGCAGCGGGAATGTGAAGAAAGAGAGAAGCGAGAAGC
TTTAGGACTAGAAAAGCAGCGGAGGAGACAAGGGCAAGAGCTATCAGCTTCACAACAGAAACCACAGGAAGACTAGGTGC
CCTGGGCTGCTGAGGAGCGCAGGAGGGAAAAGGCTGAAGAGTTAGTGGCCAGACAAAAGGTTCGAGAAAAAATTGAAAGG
GACAAAGCAGAGAGAGCCCAGAAGTATGCTGGTACTGTGGGTTCTCGGGCACCGTCGTCAGCAACAGATCCAGGTACTGT
TCCTTCTTCTCCCAGCCAGGAACCCCCTACTACGCAGGAATATGACCAATGTTGCATACAGGTTAGGCTGCCTGATGGGA
CTTCACTGACCCAAACCTTCCGGGCCCGGGAACAGCTGGCGGCTGTGAGGCTCTATGTGGAGCATCACCGTGGGGAAGAA
CCTGGACAGGACCAGGACCCTCTGCAGCTGCTCAGTGGCTTCCCCAGATGGGCTTTCTCAGAGGCTGACACGGAACAGCC
CCTGCAGAAATTGGGACTCATGCCTTCTGCTGTCCTCATCGTGGCCAAGAAGTGTCCCAGC

Alignment

ORF - retro_rnor_1601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.09 %
• Parental protein coverage: 69.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQEQTKRMLELVAQKQREREEREEREALEREKQRRRQGQELSAARQKLQEDEIRRAAEERRREKAEELAA
          R.EQT.RML..V.QKQRE.EERE.REAL..EKQRRRQGQELSA..QK.QED....AAEERRREKAEEL.A
Retrocopy RGEQTERMLGIVSQKQRECEEREKREALGLEKQRRRQGQELSASQQKPQED*VPWAAEERRREKAEELVA

Parental  RQRVREKIERDKAERAQKYGGTVGSRSSPPATDPGPVPSSPRQEPPTKREYDQCRIQVRLPDGTSLTQTF
          RQ.VREKIERDKAERAQKY.GTVGSR....ATDPG.VPSSP.QEPPT..EYDQC.IQVRLPDGTSLTQTF
Retrocopy RQKVREKIERDKAERAQKYAGTVGSRAPSSATDPGTVPSSPSQEPPTTQEYDQCCIQVRLPDGTSLTQTF

Parental  RAREQLAAVRLYVELHRGEEPGQDQDPVQLLSGFPRRAFSEADMERPLQELGLVPSAVLIVAKKCPS
          RAREQLAAVRLYVE.HRGEEPGQDQDP.QLLSGFPR.AFSEAD.E.PLQ.LGL.PSAVLIVAKKCPS
Retrocopy RAREQLAAVRLYVEHHRGEEPGQDQDPLQLLSGFPRWAFSEADTEQPLQKLGLMPSAVLIVAKKCPS

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	48.46 RPM
SRP017611_kidney	0.00 RPM	69.43 RPM
SRP017611_liver	0.00 RPM	38.66 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1601 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1601 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000019666	1 retrocopy	retro_rnor_1601 ,
Sorex araneus	ENSSARG00000008689	1 retrocopy	retro_sara_445,
Tupaia belangeri	ENSTBEG00000007971	1 retrocopy	retro_tbel_1413,