RetrogeneDB ID: retro_rnor_527

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:220440439..220441406(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vmp1
• Ensembl ID: ENSRNOG00000003967
• Aliases: Vmp1, Tmem49
• Description: Vacuole membrane protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q91ZQ0]

Sequence

>retro_rnor_527
CTTTTTCCTGCTGCTTGCTGCGCTTGTAGCTATGTGGAAGGAGCACACCAGCAGTATGTGCAGCGGATAGAGAAGTAGTT
TCTTTTATATGCCTGCTGGATAGGCCTGGGGATTCTGTCCTCCATTGGTCTCGGAACAGGATTGCACAGCTTCCTGCTTT
ATCTGGGCCCACATATAGCCTCAGTTACATTAGCTGCTTATGAATGCAATTCGGTTAATTTCCCTGAGCCACCCTATCCT
GACCAGATTATCTGCCCAGAAGAAGGCACTGAAGGAGTCATATCTTTGTGGAGTATCATCTCAAAAGTTAGAATTGAAGC
CTGCATGTGGGGCACTGGGACAGCCATTGGGGAGCTGCCTCTGTATTTCATGACCAGGGCAGCTCGCCTCTCAGGTGCTG
AACCAGATGATGAAGAGTATCAGGAATTTGAAGAAATGCTGGAACACGCAGAGACTGCACAAGACTTTGCATCACGAGCT
AAACTGGCAGTTCAAAAACTAGTACAGAAAGTTGGATTTTTTGGAATTTTGGCCTGTGCTTCTATTCCAAATCCCCTGTT
CGACCTGGCTGGAATAACATGTGGACACTTCCTTGTACCTTTTTGGACCTTCTTTGGTGCAACTCTGATTGGAAAAGCAA
TCATTAAAATGCATATCCAGAAAATCTTTGTTTATAGTAACTTTCAGCAAGCACATCGTGGAGCAGATGGTGGCTTTCAT
TGGGGCTGTACCCGGCATAGATCCGTCTCTGCAGAAGCCTTTTCAGGAATACCTGGAGGCCCAGCAACAGAAGCTCCATC
ACAGAAGTGAGGCAGGCACAGTGCAGGGAGAAAACTGGTTATCCTGGACGTTTGAGGAGCTGGTCATTGCCATAGTGTGT
TACTTTACCCTGTCTATCATTAACTCCATGGCACAGAGCTATGTCAAACAAATCCAGCAGCGCTTGAACTCAGAGGAGAA
AACTAAA

Alignment

ORF - retro_rnor_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 79.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLLAALVATYYVEGAHQQYVQRIEKQFLLYAYWIGLGILSSVGLGTGLHTFLLYLGPHIASVTLAAYECN
          L..AA..A..YVEGAHQQYVQRIEK.FLLYA.WIGLGILSS.GLGTGLH.FLLYLGPHIASVTLAAYECN
Retrocopy LFPAACCACSYVEGAHQQYVQRIEK*FLLYACWIGLGILSSIGLGTGLHSFLLYLGPHIASVTLAAYECN

Parental  SVNFPEPPYPDQIICPDEEGTEGAISLWSIISKVRIEACMWGIGTAIGELPPYFMARAARLSGAEPDDEE
          SVNFPEPPYPDQIICP.EEGTEG.ISLWSIISKVRIEACMWG.GTAIGELP.YFM.RAARLSGAEPDDEE
Retrocopy SVNFPEPPYPDQIICP-EEGTEGVISLWSIISKVRIEACMWGTGTAIGELPLYFMTRAARLSGAEPDDEE

Parental  YQEFEEMLEHAETAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITCGHFLVPFWTFFGATL
          YQEFEEMLEHAETAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITCGHFLVPFWTFFGATL
Retrocopy YQEFEEMLEHAETAQDFASRAKLAVQKLVQKVGFFGILACASIPNPLFDLAGITCGHFLVPFWTFFGATL

Parental  IGKAIIKMHIQKIFV-IVTFSKHIVEQMVAFIGAVPGIGPSLQKPFQEYLEAQRQKLHHRSEAGTAQGEN
          IGKAIIKMHIQKIFV.IVTFSKHIVEQMVAFIGAVPGI.PSLQKPFQEYLEAQ.QKLHHRSEAGT.QGEN
Retrocopy IGKAIIKMHIQKIFV>IVTFSKHIVEQMVAFIGAVPGIDPSLQKPFQEYLEAQQQKLHHRSEAGTVQGEN

Parental  WLSWTFEKLVVAMVCYFILSIINSMAQSYAKRIQQRLNSEEKTK
          WLSWTFE.LV.A.VCYF.LSIINSMAQSY.K.IQQRLNSEEKTK
Retrocopy WLSWTFEELVIAIVCYFTLSIINSMAQSYVKQIQQRLNSEEKTK

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	0.65 RPM	70.39 RPM
SRP017611_kidney	0.35 RPM	58.41 RPM
SRP017611_liver	0.40 RPM	41.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_527 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000014339	1 retrocopy	retro_mdom_2,
Mus musculus	ENSMUSG00000018171	1 retrocopy	retro_mmus_2640,
Nomascus leucogenys	ENSNLEG00000000724	1 retrocopy	retro_nleu_818,
Rattus norvegicus	ENSRNOG00000003967	1 retrocopy	retro_rnor_527 ,
Sarcophilus harrisii	ENSSHAG00000016264	1 retrocopy	retro_shar_52,
Drosophila melanogaster	FBgn0052675	1 retrocopy	retro_dmel_49,