RetrogeneDB ID: retro_mmus_2102

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:147402938..147403250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083126
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tmem254a
• Ensembl ID: ENSMUSG00000072676
• Aliases: None
• Description: transmembrane protein 254a [Source:MGI Symbol;Acc:MGI:1196450]

Sequence

>retro_mmus_2102
ACCCGGTGGGGTCGCTGCAGCTTCCAGAGGGGCACCTTGCTCTGGTTCATAGTCATCACCATCTCCTTTGGCTACTACAC
ATGGGTTGTCTTCTGGCCTCAGAGTATCCCTTAACAGAGCCTTGGGCGCCTGGGTCCCTTCACAAAGTACTTGGTGGACC
ACTATCACACCTTCCTAAGGAATGGGTATTGGCTTGCTTGGCTAATTCATGTGAGAGAGTCCTTGTATGTCTTGATTTTA
TGCAAGCGTTAAGGAATCATATACAGCCAGGCCCGGCTCCTCTGATTCCTACTGACTTTGCTGTTTGGTATA

Alignment

ORF - retro_mmus_2102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TATGAGYFQRGSLFWFTVITVSFGYYTWAVFWPQSIPYQSLGPLGPFTKYLVDHYHTFLRNGYWLAWLIH
          T..G...FQRG.L.WF.VIT.SFGYYTW.VFWPQSIP.QSLG.LGPFTKYLVDHYHTFLRNGYWLAWLIH
Retrocopy TRWGRCSFQRGTLLWFIVITISFGYYTWVVFWPQSIP*QSLGRLGPFTKYLVDHYHTFLRNGYWLAWLIH

Parental  VGESLYALVLCKRKGITDVQAQLLWFLQTFLFGV
          V.ESLY.L.LCKR.GI...QA.LL.FL.T.LFG.
Retrocopy VRESLYVLILCKR*GIIYSQARLL*FLLTLLFGI

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2102 was not detected

EST

No EST(s) were mapped for retro_mmus_2102 retrocopy.

TSS

No TSS is located nearby retro_mmus_2102 retrocopy 5' end.

Lab

retro_mmus_2102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012986	4 retrocopies	retro_amel_1410, retro_amel_1554, retro_amel_1777, retro_amel_821,
Bos taurus	ENSBTAG00000001656	1 retrocopy	retro_btau_316,
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Homo sapiens	ENSG00000133678	1 retrocopy	retro_hsap_1692,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mustela putorius furo	ENSMPUG00000003613	2 retrocopies	retro_mputfur_400, retro_mputfur_407,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102 ,
Nomascus leucogenys	ENSNLEG00000010657	1 retrocopy	retro_nleu_1337,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Pongo abelii	ENSPPYG00000002293	1 retrocopy	retro_pabe_1393,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,