RetrogeneDB ID: retro_mmus_196

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:106546811..106547060(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000059877
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Dph3
• Ensembl ID: ENSMUSG00000021905
• Aliases: Dph3, DELGIP1, DelgipP1, Desr1, KTI11, Zcsl2
• Description: DPH3 homolog (KTI11, S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1922658]

Sequence

>retro_mmus_196
ATGGCAGTATTTCATGATGAGGTGAAGAACAAGGACTTTCAATATGATGAGGACTTGGAGACCTATTTCTGTCCCTGCCC
CTGTGGGGATAGCCTCTCCATCACTAAGGAAGATTTGGAAAATGGAGAAGATGTGGCAATGTGTCCTAAGTGTTCACTCA
TTATAAAAGTGATTTATGACAAAGATCAGTTCATGTGTGGAGAAATAGTCCTAGCACCTTCAAGCAACAAAGAGTTAGTT
AGATGCTAA

Alignment

ORF - retro_mmus_196 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETYFYPCPCGDNFAITKEDLENGEDVATCPSCSLIIKVIYDKDQFMCGETV
          MAVFHDEV...DFQYDED.ETYF.PCPCGD...ITKEDLENGEDVA.CP.CSLIIKVIYDKDQFMCGE.V
Retrocopy MAVFHDEVKNKDFQYDEDLETYFCPCPCGDSLSITKEDLENGEDVAMCPKCSLIIKVIYDKDQFMCGEIV

Parental  PAPSTNKELVKC
          .APS.NKELV.C
Retrocopy LAPSSNKELVRC

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	21.54 RPM
SRP007412_cerebellum	0.00 RPM	28.35 RPM
SRP007412_heart	0.00 RPM	16.37 RPM
SRP007412_kidney	0.00 RPM	19.88 RPM
SRP007412_liver	0.00 RPM	10.35 RPM
SRP007412_testis	0.00 RPM	25.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_196 was not detected

EST

No EST(s) were mapped for retro_mmus_196 retrocopy.

TSS

No TSS is located nearby retro_mmus_196 retrocopy 5' end.

Lab

retro_mmus_196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003916	2 retrocopies	retro_btau_797, retro_btau_967,
Canis familiaris	ENSCAFG00000005881	1 retrocopy	retro_cfam_273,
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Equus caballus	ENSECAG00000016591	1 retrocopy	retro_ecab_1095,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Felis catus	ENSFCAG00000006355	1 retrocopy	retro_fcat_656,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196 ,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,