RetrogeneDB ID: retro_mmus_2190

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:95144507..95144906(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000098198
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 1110004F10Rik
• Ensembl ID: ENSMUSG00000030663
• Aliases: 1110004F10Rik, Smacp, Smap, sid2057, sid2057p
• Description: RIKEN cDNA 1110004F10 gene [Source:MGI Symbol;Acc:MGI:1929274]

Sequence

>retro_mmus_2190
CAGGAAAGAAAGAACACACTGGTCGTCTTGTTATAGGAGATCACAAATCAACATCTCACTTCTGAACAGGGGAAGAAGAC
AAGAAAATTAATGAAGAGCTGGAGTCTCAGTACCAGCAGAGCATCGACAGCAAACTGACGGTATCGGCGGCACTGCGGAC
TCGGCTTCAGTGAGGTAGAAGATCATTATGGAGAAGATGATGTGGCTAGAGATGACGATGAAGACGACTCCCCTGATGCT
GAGAGTCCAGATGACTCGGACAGTGACTCTGAGTCTGAGAAGGAGGAGTCTGCAGAAGAGCTTCATGCTGCTGAGCATCC
TGACGACACAGAAGACCCGAAGAGCAAAAAAGATGCGAAGAGCAATTATAAGATGATGTTTGTCAAGTCCAGTGGCTCC

Alignment

ORF - retro_mmus_2190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 96.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEHTGRLVIGDHKSTSHFRTGEEDKKINEELES-QYQQSMDSKLSGRYRRHCGLGFSEVEDHDGEGDVAG
          .E....LV......T....T.E..KK......S.....S..S....RYRRHCGLGFSEVEDH.GE.DVA.
Retrocopy QERKNTLVVLL*EITNQHLTSEQGKKTRKLMKSWSLSTSRASTAN*RYRRHCGLGFSEVEDHYGEDDVAR

Parental  DDDEDDSPDAESPDDSDSDSESEKEESAEELHAAEHPDDTEDPKSKKDAKSNYKMMFVKSSGS
          DDDEDDSPDAESPDDSDSDSESEKEESAEELHAAEHPDDTEDPKSKKDAKSNYKMMFVKSSGS
Retrocopy DDDEDDSPDAESPDDSDSDSESEKEESAEELHAAEHPDDTEDPKSKKDAKSNYKMMFVKSSGS

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	0.09 RPM	49.51 RPM
SRP007412_cerebellum	0.17 RPM	52.11 RPM
SRP007412_heart	0.00 RPM	33.03 RPM
SRP007412_kidney	0.02 RPM	39.06 RPM
SRP007412_liver	0.00 RPM	27.50 RPM
SRP007412_testis	0.14 RPM	45.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2190 was not detected

EST

No EST(s) were mapped for retro_mmus_2190 retrocopy.

TSS

No TSS is located nearby retro_mmus_2190 retrocopy 5' end.

Lab

retro_mmus_2190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2190 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190 , retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622,