RetrogeneDB ID: retro_mmus_2436

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:15531673..15532117(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083330
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rbm7
• Ensembl ID: ENSMUSG00000042396
• Aliases: Rbm7, 1200007M24Rik, 1500011D06Rik, AU041934, AW554393
• Description: RNA binding motif protein 7 [Source:MGI Symbol;Acc:MGI:1914260]

Sequence

>retro_mmus_2436
TCCACTGAGGCTGACTGCTCTCTAGTTATAGGCACCTAGAGTTATGGGTAATGGAGGAAATCCTCTTTGAAATATTCCAT
TGGACTAGGCCATTTCAAAAAGGTGAAAATTCCAAAAGATAAAAATAGTGAACCAAAGCAATTTGCATTTCTGAATTTCA
AATGCAAATTATTTACTGCTTTTGTGATGGATCTGCTCACTAGACCCAGACTTTTGGGGAGACCAAAACTTAGGTTAGAT
CAGGAAACAGCCATGCCTCTCAGGATGACAGTGTATAATATCCCAGCATCACTTTGGAAATTCAGACCCTATCTACGCAT
CTAGTACATCTCAAAGGACCGTGGAGAACATGACTGTGTCATTACAGATAATTCAGAGATTATCCTCTTCAGCAGAAAAT
TATCAGAGACAGCAGTAATAAACAATGTCTTGAGTCAGATGTCA

Alignment

ORF - retro_mmus_2436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.56 %
• Parental protein coverage: 56.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AAEADRTLFVG-NLETKVTEELLFELFHQAGPVIK-VKIPKDKDGKLKQFAFVNFKHEVSVPYAMNLLNG
          ..EAD..L..G..LE..V.EE.LFE.FH...P..K.VKIPKDK....KQFAF.NFK........M.LL..
Retrocopy STEADCSLVIG<HLELWVMEEILFEIFHWTRPFQK>VKIPKDKNSEPKQFAFLNFKCKLFTAFVMDLLTR

Parental  IKLFGRPIKIQF-RSGSSHASQDASVSYP-QHHVGNLSPTSTSPNSYERTVGNVSPTAQMVQRSFSSPED
          ..L.GRP.K....RSG.SHASQD.SV.YP.QHH.GN..P...S..S..RTV.N.....Q..QR..SS.E.
Retrocopy PRLLGRP-KLRL<RSGNSHASQDDSV*YP<QHHFGNSDPIYASSTS-QRTVENMTVSLQIIQRLSSSAEN

Parental  YQRQ-AVMNSVFRQMS
          YQRQ.AV.N.V..QMS
Retrocopy YQRQ<AVINNVLSQMS

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	0.00 RPM	18.76 RPM
SRP007412_cerebellum	0.00 RPM	17.28 RPM
SRP007412_heart	0.00 RPM	12.20 RPM
SRP007412_kidney	0.02 RPM	24.83 RPM
SRP007412_liver	0.00 RPM	31.40 RPM
SRP007412_testis	0.00 RPM	47.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2436 was not detected

EST

No EST(s) were mapped for retro_mmus_2436 retrocopy.

TSS

No TSS is located nearby retro_mmus_2436 retrocopy 5' end.

Lab

retro_mmus_2436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436 ,
Mus musculus	ENSMUSG00000068856	1 retrocopy	retro_mmus_1406,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,