RetrogeneDB ID: retro_mmus_2890

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:10745476..10746226(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mtfmt
• Ensembl ID: ENSMUSG00000059183
• Aliases: Mtfmt, 2310020P08Rik
• Description: mitochondrial methionyl-tRNA formyltransferase [Source:MGI Symbol;Acc:MGI:1916856]

Sequence

>retro_mmus_2890
ATACTGAATGTGCACCCCAGTTGCCTCCCGAGGTGGCATGGTTCCGCTCCAATAATCCACAAGGTGCTTCATAAAGACAC
TGTCACTGGTGTAACGATTATGCAAATTAGACTCAAAAGATTTGATATAGGCCCAATTCTCCAACAGGAAACCATCCCTG
TGCCTCCCAAGAGCACATCAAAGGAATTGGAAGCAGTGTTGTCAAAACTTGGTGCCAACATGCTTATCTCAGTTTTGAAA
AAGTTGTCTGAAAGTCTGAACAATGGAAGGCCACAGGCAACCAAGGGAGTGACAAATGCAACCAAGGTCTCTGCTGGCAC
CATCTGTGTCAAGTGGGAGGAGCAAACCTCAGAGCAAGTACTCAGACTTCACCTTGCCATTGGGGATATAGTCCCACTGC
GGATGCTGTGGATGGAGAACACCATTAAACTTCTGGATCTCATAGAAGTTAACAACTCCATTCTTGCAGATCCGAAATTA
ACAGGACAAACTGTAACTCCGAGGTCCGTGGTGTACCACAGACCATCACAAATGCTACTAGTTCACTGTAAGGATGGCTG
GATCGGTGTTCAATCACTAATGCTTAAGAAAACACTAACAGCTACTGATTTCTACAATGGATATTTGCATGTGTGGTACC
AGAAAAATTCCCACGCTCACCCAAGCCAGTGCAGATTTCAGACTCTCAGACTACCAACAAAGATACAGCAGAAAACAAGG
TTGTTGCTATGCAGCAGTGCATTAAGTAGC

Alignment

ORF - retro_mmus_2890 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.6 %
• Parental protein coverage: 64.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILNVHPSCLPRWRGPAPIIHTVLHGDTVTGVTIMQIRPKRFDIGPILQQETIPVPPKSTSKELEAVLSKL
          ILNVHPSCLPRW.G.APIIH.VLH.DTVTGVTIMQIR.KRFDIGPILQQETIPVPPKSTSKELEAVLSKL
Retrocopy ILNVHPSCLPRWHGSAPIIHKVLHKDTVTGVTIMQIRLKRFDIGPILQQETIPVPPKSTSKELEAVLSKL

Parental  GANMLISVLKNLPESLNNGRPQPAEGVTYAPKVSAGTSCVKWEEQTSEQVLRLHLAIGDIVPLQTLWMEN
          GANMLISVLK.L.ESLNNGRPQ...GVT.A.KVSAGT.CVKWEEQTSEQVLRLHLAIGDIVPL..LWMEN
Retrocopy GANMLISVLKKLSESLNNGRPQATKGVTNATKVSAGTICVKWEEQTSEQVLRLHLAIGDIVPLRMLWMEN

Parental  TVKLLDLVEVNNSILADPKLTGQTVTPGFVVYHRPSQMLLVRCKDGWIGVRSVMLKKTLTATDFYNGYLH
          T.KLLDL.EVNNSILADPKLTGQTVTP..VVYHRPSQMLLV.CKDGWIGV.S.MLKKTLTATDFYNGYLH
Retrocopy TIKLLDLIEVNNSILADPKLTGQTVTPRSVVYHRPSQMLLVHCKDGWIGVQSLMLKKTLTATDFYNGYLH

Parental  AWYQKNSHAHPSQCRFQTLRLPTKMQQKTKLLLCNSALSS
          .WYQKNSHAHPSQCRFQTLRLPTK.QQKT.LLLC.SALSS
Retrocopy VWYQKNSHAHPSQCRFQTLRLPTKIQQKTRLLLCSSALSS

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	10.77 RPM
SRP007412_cerebellum	0.00 RPM	9.03 RPM
SRP007412_heart	0.03 RPM	6.01 RPM
SRP007412_kidney	0.02 RPM	10.55 RPM
SRP007412_liver	0.00 RPM	4.83 RPM
SRP007412_testis	0.00 RPM	8.28 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2890 was not detected

EST

No EST(s) were mapped for retro_mmus_2890 retrocopy.

TSS

No TSS is located nearby retro_mmus_2890 retrocopy 5' end.

Lab

retro_mmus_2890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2890 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000059183	1 retrocopy	retro_mmus_2890 ,