RetrogeneDB ID: retro_mmus_1093

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:35990863..35991520(-)
• Located in intron of: ENSMUSG00000046573

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmed10
• Ensembl ID: ENSMUSG00000021248
• Aliases: Tmed10, 1110014C03Rik, Tmp21, p23, p24delta1
• Description: transmembrane emp24-like trafficking protein 10 (yeast) [Source:MGI Symbol;Acc:MGI:1915831]

Sequence

>retro_mmus_1093
ATGTCTGGTTTGTTTGGCCCACTCTCCCGGCCCGGCCCTCTCCCGTCCGCCTGGCTCTTTCTGTTGCTGCTCGGCCCCAG
CTCGGTCCTCGGCATCTCCTTCCATCTGCCCGTGAACTCTCGCAAGTGTCTCCGAGAGGAGATCCACAAGGACCTGCTGG
TGACGGGCGCCTACGAGATCACCGACCAGTCTGGGGGCGCTGGCGGCCTGCGCCCCCACCTCAAGATCACAGATTCTGCT
GGCCATATTCTGTATGCCAAAGAGGATGCAACCAAGGGGAAGTTTGCCTTTACCACGGAAGACTATGACATGTTTGAAGT
GTGTTTTGAGAGCAAGGGAACAGGGCAGATACCTGACCAACTCGTGATTCTAGACATGAAGCATGGAGTAGAGGCGAAAA
ATTATGAAGAGATTGCAAAAGTCGAGAAACTCAAACCACTGGAGGTGGAGTTACGACGGCTCGAGGACCTTTCCGAGTCC
ATTGTTAATGACTTTGCCTACATGAAGAAGCGGGAAGAGGAGATGAGGGACACTAATGAGTCCACGAACACCCGGGTCCT
GTACTTCAGCATCTTTTCCATGTTCTGCCTCATTGGACTAGCCACCTGGCAGGTCTTCTACCTGCGTCGCTTCTTCAAGG
CCAAGAAATTGATAGAG

Alignment

ORF - retro_mmus_1093 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGLFGPLSRPGPLPSAWLFLLLLGPSSVLGISFHLPVNSRKCLREEIHKDLLVTGAYEITDQSGGAGGL
          MSGLFGPLSRPGPLPSAWLFLLLLGPSSVLGISFHLPVNSRKCLREEIHKDLLVTGAYEITDQSGGAGGL
Retrocopy MSGLFGPLSRPGPLPSAWLFLLLLGPSSVLGISFHLPVNSRKCLREEIHKDLLVTGAYEITDQSGGAGGL

Parental  RTHLKITDSAGHILYAKEDATKGKFAFTTEDYDMFEVCFESKGTGRIPDQLVILDMKHGVEAKNYEEIAK
          R.HLKITDSAGHILYAKEDATKGKFAFTTEDYDMFEVCFESKGTG.IPDQLVILDMKHGVEAKNYEEIAK
Retrocopy RPHLKITDSAGHILYAKEDATKGKFAFTTEDYDMFEVCFESKGTGQIPDQLVILDMKHGVEAKNYEEIAK

Parental  VEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLRR
          VEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLRR
Retrocopy VEKLKPLEVELRRLEDLSESIVNDFAYMKKREEEMRDTNESTNTRVLYFSIFSMFCLIGLATWQVFYLRR

Parental  FFKAKKLIE
          FFKAKKLIE
Retrocopy FFKAKKLIE

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	0.21 RPM	94.50 RPM
SRP007412_cerebellum	0.04 RPM	76.29 RPM
SRP007412_heart	0.40 RPM	89.47 RPM
SRP007412_kidney	0.33 RPM	83.31 RPM
SRP007412_liver	0.49 RPM	76.55 RPM
SRP007412_testis	0.32 RPM	49.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1093 was not detected

EST

No EST(s) were mapped for retro_mmus_1093 retrocopy.

TSS

No TSS is located nearby retro_mmus_1093 retrocopy 5' end.

Lab

retro_mmus_1093 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1093 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016899	1 retrocopy	retro_acar_187,
Callithrix jacchus	ENSCJAG00000020627	2 retrocopies	retro_cjac_1409, retro_cjac_4223,
Dasypus novemcinctus	ENSDNOG00000019851	1 retrocopy	retro_dnov_1225,
Echinops telfairi	ENSETEG00000010607	1 retrocopy	retro_etel_1798,
Homo sapiens	ENSG00000170348	2 retrocopies	retro_hsap_2701, retro_hsap_4014,
Gorilla gorilla	ENSGGOG00000007453	1 retrocopy	retro_ggor_2696,
Myotis lucifugus	ENSMLUG00000017125	2 retrocopies	retro_mluc_2079, retro_mluc_2093,
Macaca mulatta	ENSMMUG00000015168	2 retrocopies	retro_mmul_2316, retro_mmul_885,
Mus musculus	ENSMUSG00000021248	2 retrocopies	retro_mmus_1093 , retro_mmus_649,
Nomascus leucogenys	ENSNLEG00000016453	2 retrocopies	retro_nleu_2897, retro_nleu_2963,
Oryctolagus cuniculus	ENSOCUG00000004669	1 retrocopy	retro_ocun_875,
Pongo abelii	ENSPPYG00000029389	1 retrocopy	retro_pabe_3296,
Pan troglodytes	ENSPTRG00000006552	2 retrocopies	retro_ptro_1823, retro_ptro_2724,
Rattus norvegicus	ENSRNOG00000007901	2 retrocopies	retro_rnor_1729, retro_rnor_2031,
Ictidomys tridecemlineatus	ENSSTOG00000007392	1 retrocopy	retro_itri_362,
Vicugna pacos	ENSVPAG00000003089	1 retrocopy	retro_vpac_573,