RetrogeneDB ID: retro_mmus_1387

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:33757508..33757790(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hint3
• Ensembl ID: ENSMUSG00000019791
• Aliases: None
• Description: histidine triad nucleotide binding protein 3 [Source:MGI Symbol;Acc:MGI:1914097]

Sequence

>retro_mmus_1387
TGTTTCAAAGATATCAAATCAGTGGCACTTTATCATTGTCTCGTGGTGCCAAAGAAGCATATTGGAAGTTGCAAGGATCT
AAACAAAGATCACATAGAAATGATTGAGAACATAGTAGCTGTTGGAAAAAAACCCATGCTTAAGAGGAATAATTTCACTG
ACTTCACAGATGTGAGAATGAGTTTCCATGTGGCTCTGTTCTGCTCTATCTCTCATCTGCACCTTCATGTGATAGCACTA
GTCAAAGAGTTTGGTTTCTTATCAAAGCTGGTTCACAAGAAG

Alignment

ORF - retro_mmus_1387 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.91 %
• Parental protein coverage: 56.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CFKDIKPAALYHYLVVPKKHIGSCKDLNKDHIEMVESMVAAGKT-MLERNNFTDFTDVRMGFHVPPFCSI
          CFKDIK..ALYH.LVVPKKHIGSCKDLNKDHIEM.E..VA.GK..ML.RNNFTDFTDVRM.FHV..FCSI
Retrocopy CFKDIKSVALYHCLVVPKKHIGSCKDLNKDHIEMIENIVAVGKKPMLKRNNFTDFTDVRMSFHVALFCSI

Parental  SHLHLHVIAPVKEFGFLSKLVYRQ
          SHLHLHVIA.VKEFGFLSKLV...
Retrocopy SHLHLHVIALVKEFGFLSKLVHKK

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	8.53 RPM
SRP007412_cerebellum	0.00 RPM	5.64 RPM
SRP007412_heart	0.00 RPM	14.94 RPM
SRP007412_kidney	0.00 RPM	13.99 RPM
SRP007412_liver	0.00 RPM	14.12 RPM
SRP007412_testis	0.00 RPM	5.95 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1387 was not detected

EST

No EST(s) were mapped for retro_mmus_1387 retrocopy.

TSS

No TSS is located nearby retro_mmus_1387 retrocopy 5' end.

Lab

retro_mmus_1387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001830	1 retrocopy	retro_chof_38,
Callithrix jacchus	ENSCJAG00000003710	1 retrocopy	retro_cjac_3868,
Cavia porcellus	ENSCPOG00000021856	1 retrocopy	retro_cpor_674,
Echinops telfairi	ENSETEG00000007350	1 retrocopy	retro_etel_1567,
Macropus eugenii	ENSMEUG00000007627	1 retrocopy	retro_meug_853,
Mus musculus	ENSMUSG00000019791	1 retrocopy	retro_mmus_1387 ,