RetrogeneDB ID: retro_mmus_2829

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:67565193..67566127(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mina
• Ensembl ID: ENSMUSG00000022724
• Aliases: Mina, 1810047J07Rik, 2410057H13Rik, 3830408E23Rik, AI449204
• Description: myc induced nuclear antigen [Source:MGI Symbol;Acc:MGI:1914264]

Sequence

>retro_mmus_2829
AAAAGCAAATGTGACTGTGGATCCTTAGTAGGCTCAAATGTGTTCACGTCTCCTGCAGAATCTCAGGGCCTCCCTCCACA
TTACAACAATGTTGAGGTTTTGATCCTGCAGCTGGAGGGAAAGAAACACTTGCGCCTGTACTCTCCAACTGTACCCCTGG
CACACGAGTACATTGTGGAGCCTGAGGGCCGGATTGGCACGCCAACACATGACTTCCTGCTGAAGCCTGATGGTTTGCTG
TACTTCTGCAGAGGGACCATTCATTAGGCAGAAACTCCTTCAGGCCTGGCCCACTCTATTCACCTGACTATTAGCACCTA
CCCGAACAATTCATGGGGAGATTGCCTTTTGGATTCCATTTGGGGGCTTATGTTTGACATCACAAAGGAAGATGTGGTGT
TATGACTGTAGTGCCCCAGAGGATGCTCATGAATGTGGAAACCCCAGCTGATTTAACAAGGAAGTTGAGTGGCTTTCTGG
AAACTCTTACAGACCAGCTCAAGGGCAGAAAAGAACTGCTGTCATCAGATATGAAGAAGGACTTCGTCATGCACAGACTC
GTCCTTTCTATGTGGGAAATGGAACAGAGACAATGAATCCAGGTGAAAAGTTGCCAAGGTTGGACAACATAATATGACTG
CAGTCCAAAGATCTCATTGTCCTCTCAGTAGGGGTCAGCTCAGAATCAATGTGATGAAGCTCAACAAAAGATGGTTTACA
TCTATCATTCCCTAAAGAATGCGAGACAGATGCCCATGATGGGAAAAGATGTGGAATCAGAGATTTACAGACTTCGCTTC
CCTTTATCACACATGGATGCTCTGAAGAAAATCTGGTGTGGGTCACCAATTCGTGTTAAGAGCCTGAAACTTCAAATGAA
GAAAAGGAGAGCCTGGCATTGTCTGTCTGGACAGAGTTTTTAATCCAAGTACTC

Alignment

ORF - retro_mmus_2829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 67.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KLECYFGSLVGSNVYMTPAGSQGLPPHYDDVEVFILQLEGTKHWRLYSPTVPLAHEYSVESEDRIGTPTH
          K..C..GSLVGSNV...PA.SQGLPPHY..VEV.ILQLEG.KH.RLYSPTVPLAHEY.VE.E.RIGTPTH
Retrocopy KSKCDCGSLVGSNVFTSPAESQGLPPHYNNVEVLILQLEGKKHLRLYSPTVPLAHEYIVEPEGRIGTPTH

Parental  DFLLKPGDLLYFPRGTIHQAETPSGLAYSIHLTISTYQNNSWGDCLLDSISGFVFDIAKEDVAL-RSGMP
          DFLLKP..LLYF.RGTIH.AETPSGLA.SIHLTISTY.NNSWGDCLLDSI.G..FDI.KEDV.L.....P
Retrocopy DFLLKPDGLLYFCRGTIH*AETPSGLAHSIHLTISTYPNNSWGDCLLDSIWGLMFDITKEDVVL<MTVVP

Parental  RRMLLNVETPADVTRKLSGFLRTLADQLEGREELLSSDMKKDFVKHRL-PPFFEGNGTETMDPGKQLPRL
          .RML.NVETPAD.TRKLSGFL.TL.DQL.GR.ELLSSDMKKDFV.HRL..PF..GNGTETM.PG..LPRL
Retrocopy QRMLMNVETPADLTRKLSGFLETLTDQLKGRKELLSSDMKKDFVMHRL<RPFYVGNGTETMNPGEKLPRL

Parental  DNIIRLQFKDHIVLTVGPD-KNPFDEAQQKVVYIYHSLKNVRQMHMIGEEEESEIFGLRFPLSHVDALKQ
          DNII.LQ.KD.IVL.VG....N..DEAQQK.VYIYHSLKN.RQM.M.G...ESEI..LRFPLSH.DALK.
Retrocopy DNII*LQSKDLIVLSVGVS>QNQCDEAQQKMVYIYHSLKNARQMPMMGKDVESEIYRLRFPLSHMDALKK

Parental  IWCGSPIRVKDLKL-DTDEEKENLALSLWSESLIQVL
          IWCGSPIRVK.LKL....E..E.LALS.W.E.LIQVL
Retrocopy IWCGSPIRVKSLKL<SNEEK-ESLALSVWTEFLIQVL

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	6.26 RPM
SRP007412_cerebellum	0.00 RPM	3.21 RPM
SRP007412_heart	0.00 RPM	12.73 RPM
SRP007412_kidney	0.06 RPM	13.65 RPM
SRP007412_liver	0.00 RPM	10.13 RPM
SRP007412_testis	0.23 RPM	3.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2829 was not detected

EST

No EST(s) were mapped for retro_mmus_2829 retrocopy.

TSS

No TSS is located nearby retro_mmus_2829 retrocopy 5' end.

Lab

retro_mmus_2829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015546	1 retrocopy	retro_btau_678,
Echinops telfairi	ENSETEG00000010104	1 retrocopy	retro_etel_1065,
Mus musculus	ENSMUSG00000022724	1 retrocopy	retro_mmus_2829 ,
Ochotona princeps	ENSOPRG00000015755	1 retrocopy	retro_opri_5,