RetrogeneDB ID: retro_mmus_3111

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:19580211..19580532(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 2810407C02Rik
• Ensembl ID: ENSMUSG00000075700
• Aliases: Selt, 2810407C02Rik, 5730408P04Rik
• Description: RIKEN cDNA 2810407C02 gene [Source:MGI Symbol;Acc:MGI:1916477]

Sequence

>retro_mmus_3111
CTTCAAACTGACAGGAAATTATTAATAGGTTTAATAATTGATGGCAAAGATCCTTTTGCTTTTTTCGGCATGCCAGCTTC
TAGCATCTGGCAGTGGGGCCAAGAAAATAAGGTTTATGCATGTATGATGATTTTCTTCCTGAGCAACATGATTGAGAACC
AGTGTATGTCAACAGGTGCATTTGGGATAACTTTAAATGATGTGCCAGTGTGGTCTAAGCTGGAATCTGGATATCTTCAT
TCTATGCAACAACTTGTTCAAATTCTTGACGATGAAATGAAACTCAATGTGCATATGGATTCAATCCCACATCTTCAATC
A

Alignment

ORF - retro_mmus_3111 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSVFKLVLIGLIIVGKDPFAFFGMQAPSIWQWGQENKVYACMMVFFLSNMIENQCMSTGAFEITLNDVPV
          L......LIGLII.GKDPFAFFGM.A.SIWQWGQENKVYACMM.FFLSNMIENQCMSTGAF.ITLNDVPV
Retrocopy LQTDRKLLIGLIIDGKDPFAFFGMPASSIWQWGQENKVYACMMIFFLSNMIENQCMSTGAFGITLNDVPV

Parental  WSKLESGHLPSMQQLVQILDNEMKLNVHMDSIPHHRS
          WSKLESG.L.SMQQLVQILD.EMKLNVHMDSIPH..S
Retrocopy WSKLESGYLHSMQQLVQILDDEMKLNVHMDSIPHLQS

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	0.05 RPM	137.00 RPM
SRP007412_cerebellum	0.00 RPM	114.24 RPM
SRP007412_heart	0.12 RPM	97.38 RPM
SRP007412_kidney	0.08 RPM	177.04 RPM
SRP007412_liver	0.00 RPM	118.96 RPM
SRP007412_testis	0.00 RPM	52.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3111 was not detected

EST

No EST(s) were mapped for retro_mmus_3111 retrocopy.

TSS

No TSS is located nearby retro_mmus_3111 retrocopy 5' end.

Lab

retro_mmus_3111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3111 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001394	2 retrocopies	retro_chof_1199, retro_chof_768,
Equus caballus	ENSECAG00000025123	2 retrocopies	retro_ecab_441, retro_ecab_662,
Homo sapiens	ENSG00000198843	2 retrocopies	retro_hsap_3384, retro_hsap_4126,
Gorilla gorilla	ENSGGOG00000028291	1 retrocopy	retro_ggor_1892,
Macropus eugenii	ENSMEUG00000014738	3 retrocopies	retro_meug_1766, retro_meug_1786, retro_meug_2036,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Mus musculus	ENSMUSG00000075700	1 retrocopy	retro_mmus_3111 ,
Nomascus leucogenys	ENSNLEG00000003284	2 retrocopies	retro_nleu_2473, retro_nleu_972,
Ochotona princeps	ENSOPRG00000014425	2 retrocopies	retro_opri_1052, retro_opri_584,
Pan troglodytes	ENSPTRG00000039581	1 retrocopy	retro_ptro_2804,
Rattus norvegicus	ENSRNOG00000013507	1 retrocopy	retro_rnor_2069,
Sarcophilus harrisii	ENSSHAG00000018506	1 retrocopy	retro_shar_629,
Tarsius syrichta	ENSTSYG00000007410	3 retrocopies	retro_tsyr_1515, retro_tsyr_167, retro_tsyr_46,