RetrogeneDB ID: retro_mmus_1846

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:7398423..7399077(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095690
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rab11b
• Ensembl ID: ENSMUSG00000077450
• Aliases: Rab11b, A730055L17Rik
• Description: RAB11B, member RAS oncogene family [Source:MGI Symbol;Acc:MGI:99425]

Sequence

>retro_mmus_1846
ATGGGGACCCGGGACGACGAGTACGATTACCTATTCAAAGTGGTGCTTATTGGGGACTCAGGTGTAGGTAAGAGCAACCT
GCTGTCACGCTTCACCAGAAACGAATTCAACCTAGAGAGCAAGAGTACCATCGGAGTGGAGTTCGCCACTCACAGCATTC
AGGTGGACGGCAAGACCATCAAGGCTCAGATCTGGGACACTGCTGGCCAGGAGCGCTACCGTGCCATTACCTCTGCGTAC
TACCGTGGTGCAGTGGGTGCACTGCTGGTATATGACATTGCCAAGCACTTGACATATGAGAACGTGGAGCGCTGGCTGAA
GGAGCTGCGGGATCATGCAGATAGCAACATTGTCATCATGCTGGTGGGCAACAAGAGTGACCTGCGCCACCTTCGGGCTG
TGCCCACTGATGAGGCCCGTGCCTTTGCAGAAAAGAACAACTTGTCCTTCATTGAGACCTCAGCCTTGGATTCCACCAAT
GTAGAGGAAGCATTCAAGAACATCCTCACAGAAATCTACCGTATTGTGTCACAGAAGCAAATCGCTGACCGTGCAGCCCA
CGATGAGTCCCCTGGCAACAACGTGGTGGACATCAGTGTGCCACCCACCACCGATGGACAGAGACCCAACAAGCTGCAGT
GCTGCCAGAGCCTG

Alignment

ORF - retro_mmus_1846 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQ
          MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFAT.SIQVDGKTIKAQIWDTAGQ
Retrocopy MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATHSIQVDGKTIKAQIWDTAGQ

Parental  ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEAR
          ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEAR
Retrocopy ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEAR

Parental  AFAEKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQKQIADRAAHDESPGNNVVDISVPPTTDGQRPN
          AFAEKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQKQIADRAAHDESPGNNVVDISVPPTTDGQRPN
Retrocopy AFAEKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQKQIADRAAHDESPGNNVVDISVPPTTDGQRPN

Parental  KLQCCQSL
          KLQCCQSL
Retrocopy KLQCCQSL

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	0.37 RPM	74.06 RPM
SRP007412_cerebellum	0.17 RPM	65.18 RPM
SRP007412_heart	0.40 RPM	69.26 RPM
SRP007412_kidney	0.15 RPM	49.30 RPM
SRP007412_liver	0.11 RPM	22.69 RPM
SRP007412_testis	0.18 RPM	26.80 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1846 was not detected

EST

No EST(s) were mapped for retro_mmus_1846 retrocopy.

TSS

No TSS is located nearby retro_mmus_1846 retrocopy 5' end.

Lab

retro_mmus_1846 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1846 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Mus musculus	ENSMUSG00000047187	1 retrocopy	retro_mmus_2650,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846 ,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,