RetrogeneDB ID: retro_mmus_430

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:33963354..33963659(-)
• Located in intron of: ENSMUSG00000026131

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tmem256
• Ensembl ID: ENSMUSG00000070394
• Aliases: Tmem256, 1810027O10Rik, 3110009M16Rik
• Description: transmembrane protein 256 [Source:MGI Symbol;Acc:MGI:1916436]

Sequence

>retro_mmus_430
TGGGTGGCCAGGGCAGTGCTGGTTCAGCATGTGACAACCCACAGCTTGGGCGGAGAAGGGGCTCAGTTTCTGGATGCCTA
CAGGGAGGAGCTCTTTGACAAGGCTAACAAACACTGCTTTTTGCACATCCTGACCTTGTTAGAGGTACCCTATTGCACAA
AACCCGGCTGGGCAGGTTGATGCTAGCTTCTGGAACTACCTTATCATGTACCAGCTTTTCCTACCAGGCTCCGAGTGGAG
ACATTAGCAGCCAGACTCTGGCCTGTTGTAGCCTGCTAATCTTGGGCTGGCTTACCTTGGCTTTT

Alignment

ORF - retro_mmus_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.38 %
• Parental protein coverage: 98.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WVVRAVLVPRVTTHSYG-RGAQFPDAYGKELFDKANKHHFLHSLALLGVPSCRKPVWAG-LLLASGTTLF
          WV.RAVLV..VTTHS.G..GAQF.DAY..ELFDKANKH.FLH.L.LL.VP.C.KP.WAG.L.LASGTTL.
Retrocopy WVARAVLVQHVTTHSLGGEGAQFLDAYREELFDKANKHCFLHILTLLEVPYCTKPGWAG<LMLASGTTLS

Parental  CTSFYYQALSGDTSIQTLGPVGGSLLILGWLALAF
          CTSF.YQA.SGD.S.QTL.....SLLILGWL.LAF
Retrocopy CTSFSYQAPSGDISSQTLACC--SLLILGWLTLAF

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	0.02 RPM	15.33 RPM
SRP007412_cerebellum	0.04 RPM	10.20 RPM
SRP007412_heart	0.00 RPM	19.30 RPM
SRP007412_kidney	0.00 RPM	22.98 RPM
SRP007412_liver	0.00 RPM	27.88 RPM
SRP007412_testis	0.00 RPM	0.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_430 was not detected

EST

No EST(s) were mapped for retro_mmus_430 retrocopy.

TSS

No TSS is located nearby retro_mmus_430 retrocopy 5' end.

Lab

retro_mmus_430 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_430 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016683	5 retrocopies	retro_amel_1190, retro_amel_1360, retro_amel_285, retro_amel_504, retro_amel_577,
Bos taurus	ENSBTAG00000031752	3 retrocopies	retro_btau_1301, retro_btau_1812, retro_btau_532,
Canis familiaris	ENSCAFG00000023205	2 retrocopies	retro_cfam_1146, retro_cfam_1965,
Callithrix jacchus	ENSCJAG00000037786	1 retrocopy	retro_cjac_3985,
Cavia porcellus	ENSCPOG00000004760	1 retrocopy	retro_cpor_564,
Equus caballus	ENSECAG00000016499	1 retrocopy	retro_ecab_682,
Echinops telfairi	ENSETEG00000016076	3 retrocopies	retro_etel_1865, retro_etel_2014, retro_etel_693,
Felis catus	ENSFCAG00000029899	3 retrocopies	retro_fcat_417, retro_fcat_666, retro_fcat_933,
Homo sapiens	ENSG00000205544	2 retrocopies	retro_hsap_2212, retro_hsap_687,
Gorilla gorilla	ENSGGOG00000000113	2 retrocopies	retro_ggor_1745, retro_ggor_590,
Microcebus murinus	ENSMICG00000012550	1 retrocopy	retro_mmur_841,
Macaca mulatta	ENSMMUG00000015618	2 retrocopies	retro_mmul_2408, retro_mmul_929,
Mus musculus	ENSMUSG00000070394	1 retrocopy	retro_mmus_430 ,
Nomascus leucogenys	ENSNLEG00000009435	2 retrocopies	retro_nleu_2336, retro_nleu_776,
Otolemur garnettii	ENSOGAG00000011378	1 retrocopy	retro_ogar_2039,
Ochotona princeps	ENSOPRG00000014978	2 retrocopies	retro_opri_117, retro_opri_1200,
Pongo abelii	ENSPPYG00000007915	3 retrocopies	retro_pabe_2084, retro_pabe_2179, retro_pabe_536,
Pan troglodytes	ENSPTRG00000030987	2 retrocopies	retro_ptro_1678, retro_ptro_492,
Pteropus vampyrus	ENSPVAG00000005061	1 retrocopy	retro_pvam_357,
Rattus norvegicus	ENSRNOG00000037540	2 retrocopies	retro_rnor_1592, retro_rnor_2896,
Sus scrofa	ENSSSCG00000025782	2 retrocopies	retro_sscr_160, retro_sscr_330,
Tursiops truncatus	ENSTTRG00000009794	2 retrocopies	retro_ttru_1495, retro_ttru_720,