RetrogeneDB ID: retro_mmus_2400

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:143671123..143671675(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081227
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rab6a
• Ensembl ID: ENSMUSG00000030704
• Aliases: Rab6a, 2610028L11Rik, AA419671, Rab6
• Description: RAB6A, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:894313]

Sequence

>retro_mmus_2400
CAGTGACTTGGAAAGACGTCCTTGATCACCAGATTCGTGTATGACAGTTTTGACAACACTTATCAGGCAACAATTGGCAT
TGACTTCTTATAAAAAACAATGTACTGGGAGGATCGAACTGTGCGATTGCAATTATGGGACACAGCAGGTCAAGAGAGGT
TCAGGAGCTTGATTCCTAGCTACACTCATGACTCCACTGCGGCAGTTGTTTATGATATCACAAATGTTAACTCATTCCAG
CAAACTACAAAATGGATTGATGATGTCAGAACAGAGAGAGGAAGTGATGTCATTATCATGCTAGTAGGAAATAAAACAGT
TCTTGCTGATAAGAGGCAAGTGTCAATTGAGGAGGGAGAGAGGAAAGCCAAAGAGATGAATGTTATGTTTATTGAAACCA
ATGCAAAAGCAGGATACCATGTAAAGCAGCTTTTCCAGTGTGTTGCTGCAGCTTTACCTGGAATGGAAAGCACACAGGAC
AGAATCAGAGAAGACATGATTGACATAAAACTGGAAAATCCTCAGGAGCAACCAGTCAATGAAGGCGGCTGT

Alignment

ORF - retro_mmus_2400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.81 %
• Parental protein coverage: 88.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVV
          Q..GKTSLITRF.YDSFDNTYQATIGIDFL.KTMY.EDRTVRLQLWDTAGQERFRSLIPSY..DST.A.V
Retrocopy Q*LGKTSLITRFVYDSFDNTYQATIGIDFL*KTMYWEDRTVRLQLWDTAGQERFRSLIPSYTHDSTAA-V

Parental  VYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEEGERKAKELNVMFIETSAKAGY
          VYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKT.LADKRQVSIEEGERKAKE.NVMFIET.AKAGY
Retrocopy VYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTVLADKRQVSIEEGERKAKEMNVMFIETNAKAGY

Parental  NVKQLFRRVAAALPGMESTQDRSREDMIDIKLEKPQEQPVNEGGC
          .VKQLF..VAAALPGMESTQDR.REDMIDIKLE.PQEQPVNEGGC
Retrocopy HVKQLFQCVAAALPGMESTQDRIREDMIDIKLENPQEQPVNEGGC

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	372.99 RPM
SRP007412_cerebellum	0.04 RPM	226.83 RPM
SRP007412_heart	0.09 RPM	56.35 RPM
SRP007412_kidney	0.08 RPM	70.97 RPM
SRP007412_liver	0.00 RPM	48.55 RPM
SRP007412_testis	0.00 RPM	45.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2400 was not detected

EST

No EST(s) were mapped for retro_mmus_2400 retrocopy.

TSS

No TSS is located nearby retro_mmus_2400 retrocopy 5' end.

Lab

retro_mmus_2400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2400 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175582	1 retrocopy	retro_hsap_7,
Mus musculus	ENSMUSG00000030704	1 retrocopy	retro_mmus_2400 ,
Nomascus leucogenys	ENSNLEG00000017098	1 retrocopy	retro_nleu_200,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,
Ictidomys tridecemlineatus	ENSSTOG00000023497	3 retrocopies	retro_itri_1743, retro_itri_1827, retro_itri_1885,