RetrogeneDB ID: retro_mmus_3562

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:3404836..3405184(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083918
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rbpms2
• Ensembl ID: ENSMUSG00000032387
• Aliases: Rbpms2, 2400008B06Rik, AI316523
• Description: RNA binding protein with multiple splicing 2 [Source:MGI Symbol;Acc:MGI:1919223]

Sequence

>retro_mmus_3562
AGTGGCCTCCCTGTGTATGTTAACCCTATAGCACTCTACCTGGTCTTCTGGCAGTTCAAGGTCTTTGAAGGGTCCCTGAT
CAAGCTTACCTTGAGACACACTCATGGTTTTCTGAACTTTGACAGCCCAGCATTAACAGAAGCATCCAAACTCACATTCA
ATGTTATTCACTTTGATCTGGAGAACCGATAGACCCTGAGGCTAGAGTTTGCCAAAGCCAACAGCAAGATAGCAAAGAGC
AAACTAATAGTGACACCAAATCCCACCAATGTCCACCCTGCCCTAGGAGCACACTTGATCACAAGGGACTCTTATGACCT
TATGGGAGCTGCTATGATTCCTGCATCC

Alignment

ORF - retro_mmus_3562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 56.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGLPVDIKPRELYLLFRPFKGYEGSLIKLTSRQPVGFVIFDSRAGAEAAKNALNGIRFDPENPQTLRLEF
          SGLPV...P..LYL.F..FK..EGSLIKLT.R...GF..FDS.A..EA.K...N.I.FD.EN..TLRLEF
Retrocopy SGLPVYVNPIALYLVFWQFKVFEGSLIKLTLRHTHGFLNFDSPALTEASKLTFNVIHFDLENR*TLRLEF

Parental  AKANTKMAKSKLIATPNPTSVHPALGAHLIARDPYDLMGTALIPAS
          AKAN.K.AKSKLI.TPNPT.VHPALGAHLI.RD.YDLMG.A.IPAS
Retrocopy AKANSKIAKSKLIVTPNPTNVHPALGAHLITRDSYDLMGAAMIPAS

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	1.89 RPM
SRP007412_cerebellum	0.00 RPM	2.91 RPM
SRP007412_heart	0.00 RPM	29.85 RPM
SRP007412_kidney	0.00 RPM	61.16 RPM
SRP007412_liver	0.00 RPM	38.97 RPM
SRP007412_testis	0.00 RPM	3.70 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3562 was not detected

EST

No EST(s) were mapped for retro_mmus_3562 retrocopy.

TSS

No TSS is located nearby retro_mmus_3562 retrocopy 5' end.

Lab

retro_mmus_3562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562 , retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,