RetrogeneDB ID: retro_mmus_2387

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:112537060..112537660(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dnttip1
• Ensembl ID: ENSMUSG00000017299
• Aliases: None
• Description: deoxynucleotidyltransferase, terminal, interacting protein 1 [Source:MGI Symbol;Acc:MGI:1923483]

Sequence

>retro_mmus_2387
ATGGGGGTGACTGGTGACACCAAGCAGCCACAGAGCCCTGGAGGGGCAGAGCTAGGTGGCCTGGAGCTGGGCGACGTGGG
CGTGGCGGGCCAGCCAGTTCTCAGGAACCCTTGGAACATAATGATAAAACACTGTCAGGTGCAGCGAAGGGGCCGCCGAT
CTCAGATGATCACAAGTTTCACAATCCCAGCCATCTCTATGGATCTCCTCTGTGCTGTCCTGCAGCCTAGCATCAATGAG
GAGATCCAGAGTGTCTTCAACAAGTACATGAAGTTCTTCCAGAAGGCAGTGCTGAATGTGTGAGACAATGTTGGGGAAGA
AGTGGACGCAGAGCAGTTGATTCAGGAGGCCTGCCACAGCTGCCTGGAGCAGGTAAAGCTGCTCTTTTCTGATGGAGAGA
AAGTGATACCCACATTGGCCCATGAGCTTCCAGGGATCAAGCAGGGCCAGCAAGCAGCAGAGGAGTCCCACCGAGGAAGC
CCCATTCCCAAAAAGAGGAAAGGTCGGCCTCCTGGACATGTCCTGTCGAATGACCACATAGCTGCTGCCATGGTATGGAA
ACCAAAATCCTGTGAACCAATTCGCCGAGAAGGCCCCAAG

Alignment

ORF - retro_mmus_2387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 94.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGATGDTEQPRGPGGAERGGLELGDAGAAGQPVLTNPWNIMIKHRQVQRRGRRSQMTTSFTDPAISMDLL
          MG.TGDT.QP..PGGAE.GGLELGD.G.AGQPVL.NPWNIMIKH.QVQRRGRRSQM.TSFT.PAISMDLL
Retrocopy MGVTGDTKQPQSPGGAELGGLELGDVGVAGQPVLRNPWNIMIKHCQVQRRGRRSQMITSFTIPAISMDLL

Parental  RAVLQPSINEEIQGVFNKYMKFFQKAALNVRDNVGEEVDAEQLIQEACRSCLEQAKLLFSDGEKVIPRLA
          .AVLQPSINEEIQ.VFNKYMKFFQKA.LNV.DNVGEEVDAEQLIQEAC.SCLEQ.KLLFSDGEKVIP.LA
Retrocopy CAVLQPSINEEIQSVFNKYMKFFQKAVLNV*DNVGEEVDAEQLIQEACHSCLEQVKLLFSDGEKVIPTLA

Parental  HELPGIKRGRQAEEESHRGSPIPKKRKGRPPGHVLSNDRAAAGMVWKQKSCEPIRREGPK
          HELPGIK.G.QA.EESHRGSPIPKKRKGRPPGHVLSND..AA.MVWK.KSCEPIRREGPK
Retrocopy HELPGIKQGQQAAEESHRGSPIPKKRKGRPPGHVLSNDHIAAAMVWKPKSCEPIRREGPK

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	11.84 RPM
SRP007412_cerebellum	0.00 RPM	12.72 RPM
SRP007412_heart	0.00 RPM	11.05 RPM
SRP007412_kidney	0.00 RPM	10.18 RPM
SRP007412_liver	0.00 RPM	6.66 RPM
SRP007412_testis	0.05 RPM	22.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2387 was not detected

EST

No EST(s) were mapped for retro_mmus_2387 retrocopy.

TSS

No TSS is located nearby retro_mmus_2387 retrocopy 5' end.

Lab

retro_mmus_2387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000017299	1 retrocopy	retro_mmus_2387 ,
Pteropus vampyrus	ENSPVAG00000000368	1 retrocopy	retro_pvam_1217,
Sarcophilus harrisii	ENSSHAG00000002289	1 retrocopy	retro_shar_514,