RetrogeneDB ID: retro_mmus_1130

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:89577157..89578413(-)
• Located in intron of: ENSMUSG00000021613

Retrocopy information

• Ensembl ID: ENSMUSG00000094463
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Agk
• Ensembl ID: ENSMUSG00000029916
• Aliases: Agk, 2610037M15Rik, 6720408I04Rik, AI465370, Mulk
• Description: acylglycerol kinase [Source:MGI Symbol;Acc:MGI:1917173]

Sequence

>retro_mmus_1130
TTCTTTAAAACGCTTCGAAATCATTGGAAGAAAACTATAGCTGGGCTCTGTTTGCTGACATGGGGAGGTCACTGGCTCTA
CGGGAAGCACTGTGATAACCTGCTAAGAAGAGCAGCCTGTCAAGAAGCTCAGGTGTTTGGCAACCAGCTCATTCCTCCCA
ATGCACAAGTGAAGAAAGCCACCGTCTTTCTCAATCCCGCAGCTTGCAAAGGCAAAGCCAGAACTCTATTTGAAAAAAAT
ACTGCTCCAATTTTACACCTGTCTGGCATGGATGTGACTGTTGTCAAGATGGATTATGAGGGACAAGCCAAGAAGCTCCT
GGAGTTGATGGAAAGCACTGATGTGATCATTGTTGCTGGAGGAGACGGCACACTGCAGGAGGTTGTTACTGGAGTACTGA
GAAGAACAGATGAGGCTACCTTCAGTAAGATTCCAATTGGATTTATCCCGCTGGGACAGACCAGTAGTTTGAGTCACACT
CTCTTTGCTGAAAGTGGAAACAAAGTCCAACATATTTTCAGACGCCACACTTGCCATTGTGAAAGGAGAGACTGTTCCAC
TTGATGTCTTGCAGATCAAGGGTGAAAAAGAACAACCTGTGTATGCAATGACTGGCCTCCGGTGGGGGATCCTTCAGAGA
TGCTGGCGTCAAAGTTAGCAAGTACTGGTATCTTGGTCCACTAAAAACCAAAGCAGCCCACTTTTTCAGCACTCTTCAGG
AATGGCCTCAGACTCATCAAGCCTCCATCTCTTACACGGGACCTAGAGAGAGACCTCCCATTGAGCCTGAAGAGACTCCT
CCCAGGCCGTCTCTGTATAGGAGAATATTACGCAGGCTTGCCTCATTCTGGGCACAGCCACAGGATGCCTCCTCCCGAGA
GGTAAGCCCTGAGGTCTGGAAAGATGTACAACTGTCCACCATTGAACTGTCCATCACAACCCGAAACACCCAGCTTGACC
TGATGAGCAAAGAGGATTTTATGAACATTTGCATTGAACCTGACACTGTCAGCAAAGGAGATTTCATAATCATAGGAAGT
AAGAAGGTGAGAGACCCTGGCCTGCGTGCAGCTGGCACCGAGTGCCTCCAAGCCAGCCACTGTACTCTGGTTCTTCCTGA
GGGAACTGAGGGCTCCTTCAGCATTGACAGCGAGGAGTACGAAGCCATGCCGGTGGAGGTCAAACTACTGCCCAGAAAGC
TGCGGTTCTTCTGTGATCCGAGGAAGAGAGAGCAAATGCTGCCGAGCACATCCCAG

Alignment

ORF - retro_mmus_1130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.57 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FFKTLRNHWKKTTAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPAACK
          FFKTLRNHWKKT.AGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPAACK
Retrocopy FFKTLRNHWKKTIAGLCLLTWGGHWLYGKHCDNLLRRAACQEAQVFGNQLIPPNAQVKKATVFLNPAACK

Parental  GKARTLFEKNAAPILHLSGMDVTVVKTDYEGQAKKLLELMESTDVIIVAGGDGTLQEVVTGVLRRTDEAT
          GKARTLFEKN.APILHLSGMDVTVVK.DYEGQAKKLLELMESTDVIIVAGGDGTLQEVVTGVLRRTDEAT
Retrocopy GKARTLFEKNTAPILHLSGMDVTVVKMDYEGQAKKLLELMESTDVIIVAGGDGTLQEVVTGVLRRTDEAT

Parental  FSKIPIGFIPLGQTSSLSHTLFAESGNKVQHI-TDATLAIVKGETVPLDVLQIKGEKEQPVYAMTGLRW-
          FSKIPIGFIPLGQTSSLSHTLFAESGNKVQHI..DATLAIVKGETVPLDVLQIKGEKEQPVYAMTGLRW.
Retrocopy FSKIPIGFIPLGQTSSLSHTLFAESGNKVQHI>SDATLAIVKGETVPLDVLQIKGEKEQPVYAMTGLRW>

Parental  GSFRDAGVKVSKYWYLGPLKTKAAHFFSTLQEWPQTHQASISYTGPRERPPIEPEETPPRPSLYRRILRR
          GSFRDAGVKVSKYWYLGPLKTKAAHFFSTLQEWPQTHQASISYTGPRERPPIEPEETPPRPSLYRRILRR
Retrocopy GSFRDAGVKVSKYWYLGPLKTKAAHFFSTLQEWPQTHQASISYTGPRERPPIEPEETPPRPSLYRRILRR

Parental  LASFWAQPQDASSREVSPEVWKDVQLSTIELSITTRNTQLDLMSKEDFMNICIEPDTVSKGDFIIIGSKK
          LASFWAQPQDASSREVSPEVWKDVQLSTIELSITTRNTQLDLMSKEDFMNICIEPDTVSKGDFIIIGSKK
Retrocopy LASFWAQPQDASSREVSPEVWKDVQLSTIELSITTRNTQLDLMSKEDFMNICIEPDTVSKGDFIIIGSKK

Parental  VRDPGLRAAGTECLQASHCTLVLPEGTEGSFSIDSEEYEAMPVEVKLLPRKLRFFCDPRKREQMLPSTSQ
          VRDPGLRAAGTECLQASHCTLVLPEGTEGSFSIDSEEYEAMPVEVKLLPRKLRFFCDPRKREQMLPSTSQ
Retrocopy VRDPGLRAAGTECLQASHCTLVLPEGTEGSFSIDSEEYEAMPVEVKLLPRKLRFFCDPRKREQMLPSTSQ

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	0.61 RPM	12.55 RPM
SRP007412_cerebellum	1.13 RPM	9.94 RPM
SRP007412_heart	0.19 RPM	7.81 RPM
SRP007412_kidney	0.58 RPM	5.99 RPM
SRP007412_liver	0.22 RPM	2.40 RPM
SRP007412_testis	0.50 RPM	3.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1130 was not detected

EST

No EST(s) were mapped for retro_mmus_1130 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_31434	47 libraries	22 libraries	441 libraries	492 libraries	70 libraries

The graphical summary, for retro_mmus_1130 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013589	1 retrocopy	retro_cjac_3228,
Gorilla gorilla	ENSGGOG00000008821	1 retrocopy	retro_ggor_3061,
Loxodonta africana	ENSLAFG00000002479	1 retrocopy	retro_lafr_403,
Microcebus murinus	ENSMICG00000002561	1 retrocopy	retro_mmur_850,
Macaca mulatta	ENSMMUG00000021017	1 retrocopy	retro_mmul_2637,
Mus musculus	ENSMUSG00000029916	1 retrocopy	retro_mmus_1130 ,
Nomascus leucogenys	ENSNLEG00000002291	1 retrocopy	retro_nleu_2349,
Pongo abelii	ENSPPYG00000018064	1 retrocopy	retro_pabe_3812,
Pan troglodytes	ENSPTRG00000019775	2 retrocopies	retro_ptro_3269, retro_ptro_3311,