RetrogeneDB ID: retro_mmus_1933

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:72633935..72634604(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081957
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ak4
• Ensembl ID: ENSMUSG00000028527
• Aliases: Ak4, AK 4, Ak-3, Ak-4, Ak3, Ak3l1, D4Ertd274e
• Description: adenylate kinase 4 [Source:MGI Symbol;Acc:MGI:87979]

Sequence

>retro_mmus_1933
ATGGCTTCCAAACTCCTGCGCGCGGTCATCCTCGGACCGCCCGGCTCTGGCAAGGGCACCGTTTGCGAAAGGATCGCCCA
GAACTTTGGCCTCCAGCATCTCTCCAGCGGCCACTTGTTGCGGGAGAACCTCAAGACCGGCACGGAAGTTGGTGACGTGG
CAAAACAGTACCTAGAAAAAGGTCTTTTGGTTCCAGATCACGTGATCACACGCCTAATGATGTCAGAACTGGAGACTCGG
AGTGCCCAGCACTGGCTGTTAGATGGATTCCCGAGGACATTAGTGCAGGCAGAAGCCCTGGACGGAATCTGTGATGTGGA
CCTAGTAATCAGTTTGAATATTCCTTTTGAGACACTTAAAGATCGTCTGAGCCGACGATGGATTCACCCTTCTAGCGGGA
GGGTCTATAACCTGGACTTCAACCCACCTCAAGTGCAGGGGATTGATGACATCACTGGTGAGCCACTTGTCCAACAGGAA
GATGATAAACCTGAAGCAGTTGCTGCCAGGCTAAGACGGTACAAGGATGCGGCAAAACCAGTCATCGAACTGTACAAGAG
CCGTGGAGTGCTCCACCAGTTTTCTGGGACGGAGACTAACAGAATCTGGCCTTATGTTTACACACTTTTCTCCAACAAGA
TCACACCTATTCAATCCAAAGAAGCCTAC

Alignment

ORF - retro_mmus_1933 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKLLRAVILGPPGSGKGTVCERIAQNFGLQHLSSGHLLRENLKTGTEVGDVAKQYLEKGLLVPDHVIT
          MASKLLRAVILGPPGSGKGTVCERIAQNFGLQHLSSGHLLRENLKTGTEVGDVAKQYLEKGLLVPDHVIT
Retrocopy MASKLLRAVILGPPGSGKGTVCERIAQNFGLQHLSSGHLLRENLKTGTEVGDVAKQYLEKGLLVPDHVIT

Parental  RLMMSELETRSAQHWLLDGFPRTLVQAEALDGICDVDLVISLNIPFETLKDRLSRRWIHPSSGRVYNLDF
          RLMMSELETRSAQHWLLDGFPRTLVQAEALDGICDVDLVISLNIPFETLKDRLSRRWIHPSSGRVYNLDF
Retrocopy RLMMSELETRSAQHWLLDGFPRTLVQAEALDGICDVDLVISLNIPFETLKDRLSRRWIHPSSGRVYNLDF

Parental  NPPQVQGIDDITGEPLVQQEDDKPEAVAARLRRYKDAAKPVIELYKSRGVLHQFSGTETNRIWPYVYTLF
          NPPQVQGIDDITGEPLVQQEDDKPEAVAARLRRYKDAAKPVIELYKSRGVLHQFSGTETNRIWPYVYTLF
Retrocopy NPPQVQGIDDITGEPLVQQEDDKPEAVAARLRRYKDAAKPVIELYKSRGVLHQFSGTETNRIWPYVYTLF

Parental  SNKITPIQSKEAY
          SNKITPIQSKEAY
Retrocopy SNKITPIQSKEAY

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	37.68 RPM
SRP007412_cerebellum	0.00 RPM	62.40 RPM
SRP007412_heart	0.12 RPM	33.22 RPM
SRP007412_kidney	0.46 RPM	321.62 RPM
SRP007412_liver	0.08 RPM	105.93 RPM
SRP007412_testis	0.00 RPM	4.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1933 was not detected

EST

2 EST(s) were mapped to retro_mmus_1933 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BY330553	72634011	72634179	95.9	166	2	162
CK640369	72634077	72634312	97.5	227	5	220

TSS

No TSS is located nearby retro_mmus_1933 retrocopy 5' end.

Lab

retro_mmus_1933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1933 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016835	1 retrocopy	retro_cjac_1856,
Homo sapiens	ENSG00000162433	6 retrocopies	retro_hsap_1101, retro_hsap_1744, retro_hsap_2993, retro_hsap_3320, retro_hsap_3619, retro_hsap_4225,
Gorilla gorilla	ENSGGOG00000026644	4 retrocopies	retro_ggor_1301, retro_ggor_2073, retro_ggor_2444, retro_ggor_2829,
Myotis lucifugus	ENSMLUG00000009622	1 retrocopy	retro_mluc_1708,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080,
Mus musculus	ENSMUSG00000028527	1 retrocopy	retro_mmus_1933 ,
Nomascus leucogenys	ENSNLEG00000015163	3 retrocopies	retro_nleu_1666, retro_nleu_2481, retro_nleu_743,
Otolemur garnettii	ENSOGAG00000016024	1 retrocopy	retro_ogar_3375,
Ochotona princeps	ENSOPRG00000010345	17 retrocopies	retro_opri_1094, retro_opri_153, retro_opri_291, retro_opri_328, retro_opri_357, retro_opri_417, retro_opri_438, retro_opri_442, retro_opri_666, retro_opri_724, retro_opri_73, retro_opri_743, retro_opri_752, retro_opri_765, retro_opri_889, retro_opri_892, retro_opri_947,
Pongo abelii	ENSPPYG00000001269	6 retrocopies	retro_pabe_1021, retro_pabe_2479, retro_pabe_2735, retro_pabe_2970, retro_pabe_3412, retro_pabe_3483,
Pan troglodytes	ENSPTRG00000000827	4 retrocopies	retro_ptro_2024, retro_ptro_2154, retro_ptro_2449, retro_ptro_2870,