RetrogeneDB ID: retro_mmus_2557

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:29538152..29538506(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000078182
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dppa5a
• Ensembl ID: ENSMUSG00000060461
• Aliases: Dppa5a, AA536857, Dppa5, Esg1, ecat2
• Description: developmental pluripotency associated 5A [Source:MGI Symbol;Acc:MGI:101800]

Sequence

>retro_mmus_2557
ATGATGGTAACCCTCATGACCCGTAAAGACATCCCCCCGTGGGTGAAAGTTCCTGAAGACCTGAAAGATCCAGAAGTATT
CCAGGTCCAGTCGCTGGTACTGAAATCTCTGTTTGGCCCACAGGGATCTCGAATGTCTCACATTGAGCAGGTGAGCCAGG
CCATGTTTGAGCTGAAGAACCTGGAATCTCCCGAAGAACTTATCGAGGTCTTCCTTTACGGCTCTCAAAACAACAAGGTT
CTGGCTAAATGGATACTTCAGTCCATGGCTGAGAGGTACCGCCTGCGCCAGCAAAAAGGAGTGCTGAAGCTGGAGGAATC
CATGAAGACCCTGGAGCTAGGCCAGTGTATCGAG

Alignment

ORF - retro_mmus_2557 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMVTLVTRKDIPPWVKVPEDLKDPEVFQVQSLVLKYLFGPQGSRMSHIEQVSQAMFELKNLESPEELIEV
          MMVTL.TRKDIPPWVKVPEDLKDPEVFQVQSLVLK.LFGPQGSRMSHIEQVSQAMFELKNLESPEELIEV
Retrocopy MMVTLMTRKDIPPWVKVPEDLKDPEVFQVQSLVLKSLFGPQGSRMSHIEQVSQAMFELKNLESPEELIEV

Parental  FIYGSQNNKIRAKWMLQSMAERYHLRQQKGVLKLEESMKTLELGQCIE
          F.YGSQNNK..AKW.LQSMAERY.LRQQKGVLKLEESMKTLELGQCIE
Retrocopy FLYGSQNNKVLAKWILQSMAERYRLRQQKGVLKLEESMKTLELGQCIE

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.02 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.09 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2557 was not detected

EST

No EST(s) were mapped for retro_mmus_2557 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_113076	1037 libraries	5 libraries	14 libraries	14 libraries	2 libraries

The graphical summary, for retro_mmus_2557 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_2557 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2557 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002647	2 retrocopies	retro_cfam_1216, retro_cfam_524,
Choloepus hoffmanni	ENSCHOG00000012338	1 retrocopy	retro_chof_2495,
Callithrix jacchus	ENSCJAG00000009945	3 retrocopies	retro_cjac_1978, retro_cjac_62, retro_cjac_85,
Dasypus novemcinctus	ENSDNOG00000011544	4 retrocopies	retro_dnov_115, retro_dnov_15, retro_dnov_2318, retro_dnov_53,
Dipodomys ordii	ENSDORG00000000378	2 retrocopies	retro_dord_324, retro_dord_690,
Homo sapiens	ENSG00000203909	1 retrocopy	retro_hsap_2067,
Gorilla gorilla	ENSGGOG00000012001	1 retrocopy	retro_ggor_1489,
Myotis lucifugus	ENSMLUG00000004463	1 retrocopy	retro_mluc_1051,
Macaca mulatta	ENSMMUG00000000417	1 retrocopy	retro_mmul_1409,
Mus musculus	ENSMUSG00000060461	7 retrocopies	retro_mmus_127, retro_mmus_1280, retro_mmus_1537, retro_mmus_1666, retro_mmus_2557 , retro_mmus_3415, retro_mmus_58,
Pongo abelii	ENSPPYG00000016771	1 retrocopy	retro_pabe_1680,
Pan troglodytes	ENSPTRG00000029547	1 retrocopy	retro_ptro_1380,
Rattus norvegicus	ENSRNOG00000000199	3 retrocopies	retro_rnor_106, retro_rnor_28, retro_rnor_76,
Sus scrofa	ENSSSCG00000004283	2 retrocopies	retro_sscr_190, retro_sscr_487,
Ictidomys tridecemlineatus	ENSSTOG00000005326	2 retrocopies	retro_itri_199, retro_itri_703,