RetrogeneDB ID: retro_mmus_2081

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:116527845..116528490(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081787
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rab5b
• Ensembl ID: ENSMUSG00000000711
• Aliases: Rab5b, C030027M18Rik
• Description: RAB5B, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:105938]

Sequence

>retro_mmus_2081
ATGACTAGCAGAAGTACAGCCAGGCCCAATGGGCAACCCCAGGCCAGCAAAATATGCCAGTTCAAATTGGTCCTGCTGGG
AGAGTCTGCAGTGGGGAAGTCTAGCCTGGTGTTACGTTTTGTCAAAGGACAGTTCCATGAATACCAGGAAAGCACCATTG
GAGCGGCCTTCCTCACCCAATCCGTGTGTCTAGATGACACAACAGTCAAGTTTGAGATCTGGGACACTGCTGGGCAGGAG
CGATACCACAGTTTAGCCCCTATGTACTACAGGGGTGCCCAGGCTGCAATCGTGGTCTATGATATTACTAATCAGGAAAC
GTTTGCTCGGGCAAAGACATGGGTAAAGGAACTACAGCGGCAAGCCAGCCCCAGCATTGTTATTGCCTTGGCAGGGAACA
AAGCTGACCTTGCCAACAAGCGCATGGTGGAGTATGAAGAGGCTCAGGCATATGCAGATGACAACAGCTTATTATTTATG
GAGACTTCAGCTAAGACTGCTATGAACGTGAATGATCTCTTCCTGGCAATAGCAAAGAAGTTGCCAAAGAGTGAACCCCA
GAATCTGGGGGGTGCGGCAGGCCGAAGTCGGGGCGTGGATCTTCATGAGCAGTCCCAGCAGAACAAGAGCCAGTGTTGTA
GCAAC

Alignment

ORF - retro_mmus_2081 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSRSTARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVK
          MTSRSTARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVK
Retrocopy MTSRSTARPNGQPQASKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQSVCLDDTTVK

Parental  FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANK
          FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANK
Retrocopy FEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNQETFARAKTWVKELQRQASPSIVIALAGNKADLANK

Parental  RMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQNKS
          RMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQNKS
Retrocopy RMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLFLAIAKKLPKSEPQNLGGAAGRSRGVDLHEQSQQNKS

Parental  QCCSN
          QCCSN
Retrocopy QCCSN

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
SRP007412_brain	0.14 RPM	69.29 RPM
SRP007412_cerebellum	0.04 RPM	69.78 RPM
SRP007412_heart	0.09 RPM	50.43 RPM
SRP007412_kidney	0.10 RPM	65.74 RPM
SRP007412_liver	0.03 RPM	56.72 RPM
SRP007412_testis	0.00 RPM	21.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2081 was not detected

EST

No EST(s) were mapped for retro_mmus_2081 retrocopy.

TSS

No TSS is located nearby retro_mmus_2081 retrocopy 5' end.

Lab

retro_mmus_2081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2081 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081 ,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,