RetrogeneDB ID: retro_mmus_2007

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:9041119..9041665(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082953
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Slc25a36
• Ensembl ID: ENSMUSG00000032449
• Aliases: Slc25a36, C330005L02Rik
• Description: solute carrier family 25, member 36 [Source:MGI Symbol;Acc:MGI:1924909]

Sequence

>retro_mmus_2007
TTTACTGCAATCACTGCAACAAACCCCATTTGGCTTATAAAGACTCGCTTACAGCTTGATGCAAGGACTCGTGGGGAAAA
GCAAATGGGTGCTTTTGAATGTGTTCGTAAAGTCTATCAGACAGACGGACTGCGAGGATTTTATAGGGGCATGTCTGCCT
CCTATGCCGGCATATCAGAGACTGTTATCCATTTTGTTATTTATGAAAGTATAAAGCAAAAACTACTGGAATGTAAGACT
GCTTCTATGATGGAAACTGATGAGGAGTCTGTGAAAGAAGCATCGGATTTTGTGAGAATGATGCTAGCTGCTGCCACCTC
AAAAACCTCTGCCACAACCATAGCGTATCCACATGAAGTTGTAAGAACAAGACTACGTGAAGAAGGGACAAAATATAGGT
CTTTTTTTCAAACATTGTCTTTGATTGTTCAAGAAGAAGGCTATGGATCTCTTTACCGCGGTCTAACAACTCATCTGGTG
AGGCAGATTCCAAACACGGCCATTATGATGGCCACCTACGAACTGGTGGTCTACCTTCTCAACGGA

Alignment

ORF - retro_mmus_2007 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.45 %
• Parental protein coverage: 58.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTAITATNPIWLIKTRLQLDARTRGEKQMGAFECVRKVYQTDGLRGFYRGMSASYAGISETVIHFVIYES
          FTAITATNPIWLIKTRLQLDARTRGEKQMGAFECVRKVYQTDGLRGFYRGMSASYAGISETVIHFVIYES
Retrocopy FTAITATNPIWLIKTRLQLDARTRGEKQMGAFECVRKVYQTDGLRGFYRGMSASYAGISETVIHFVIYES

Parental  IKQKLLECKTASMMETDEESVKEASDFVRMMLAAATSKTCATTIAYPHEVVRTRLREEGTKYRSFFQTLS
          IKQKLLECKTASMMETDEESVKEASDFVRMMLAAATSKT.ATTIAYPHEVVRTRLREEGTKYRSFFQTLS
Retrocopy IKQKLLECKTASMMETDEESVKEASDFVRMMLAAATSKTSATTIAYPHEVVRTRLREEGTKYRSFFQTLS

Parental  LIVQEEGYGSLYRGLTTHLVRQIPNTAIMMATYELVVYLLNG
          LIVQEEGYGSLYRGLTTHLVRQIPNTAIMMATYELVVYLLNG
Retrocopy LIVQEEGYGSLYRGLTTHLVRQIPNTAIMMATYELVVYLLNG

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	51.84 RPM
SRP007412_cerebellum	0.00 RPM	39.60 RPM
SRP007412_heart	0.03 RPM	29.45 RPM
SRP007412_kidney	0.04 RPM	83.35 RPM
SRP007412_liver	0.00 RPM	3.11 RPM
SRP007412_testis	0.00 RPM	15.83 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2007 was not detected

EST

No EST(s) were mapped for retro_mmus_2007 retrocopy.

TSS

No TSS is located nearby retro_mmus_2007 retrocopy 5' end.

Lab

retro_mmus_2007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2007 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000010094	1 retrocopy	retro_ecab_234,
Felis catus	ENSFCAG00000027489	1 retrocopy	retro_fcat_1680,
Macaca mulatta	ENSMMUG00000022153	1 retrocopy	retro_mmul_2243,
Mus musculus	ENSMUSG00000032449	1 retrocopy	retro_mmus_2007 ,
Oryctolagus cuniculus	ENSOCUG00000002085	1 retrocopy	retro_ocun_361,
Pteropus vampyrus	ENSPVAG00000007958	1 retrocopy	retro_pvam_719,
Sus scrofa	ENSSSCG00000011669	1 retrocopy	retro_sscr_871,
Tupaia belangeri	ENSTBEG00000001759	1 retrocopy	retro_tbel_3349,
Tursiops truncatus	ENSTTRG00000003288	2 retrocopies	retro_ttru_1146, retro_ttru_947,
Vicugna pacos	ENSVPAG00000008292	1 retrocopy	retro_vpac_603,