RetrogeneDB ID: retro_mmus_75

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:37637676..37638474(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000050304
• Aliases: Slc25a2, Ornt2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Slc25a15
• Ensembl ID: ENSMUSG00000031482
• Aliases: Slc25a15, D630044L02Rik, Ornt1
• Description: solute carrier family 25 (mitochondrial carrier ornithine transporter), member 15 [Source:MGI Symbol;Acc:MGI:1342274]

Sequence

>retro_mmus_75
ATGCAGACATTTCCTCAGCTGTACAAAGGCCTTGCCGACTGCTTCCTGAAAACATACAACCAAGTGGGCATCCGTGGCCT
TTACAGGGGAACCAGTCCTGCACTGCTAGCCTATGTCACCCAGGGTTCTGTCCTGTTCATGTGCTTTGGCTTTTGCCAAC
AGTTTGTCAGGAAAGTGGCTAGAGTGGAGCAGAATGCAGAGCTGAACGACTTGGAGACTGCTACTGCTGGGTCGCTGGCT
TCTGCATTTGCTGCGCTGGCTCTCTGCCCCACTGAGCTTGTGAAGTGTCGGCTGCAGACCATGTATGAGATGAAGATGTC
AGGGAAGATAGCACAAAGCTATAACACAATTTGGTCTATGGTTAAGAGTATCTTCATGAAGGATGGTCCCTTAGGCTTCT
ATCGTGGACTCTCGACCACTCTTGCTCAGGAAATACCTGGCTATTTCTTCTACTTTGGGGGCTATGAAATCAGTCGATCA
TTTTTTGCATCAGGGGGATCAAAGGATGAACTAGGCCCTGTCCCTTTGATGTTAAGTGGAGGCTTTGCTGGGATCTGTCT
CTGGCTTATCATATTCCCAGTGGACTGCATTAAATCCAGAATCCAGGTTCTTTCTATGTTTGGGAAGCCTGCAGGATTAA
TCGAAACCTTTATAAGTGTTGTGAGAAATGAAGGGATATCAGCCTTGTATTCTGGATTGAAAGCCACTCTGATTCGAGCC
ATCCCTTCCAATGCTGCTCTCTTTTTGGTTTATGAGTACAGCAGAAAGATGATGATGAACATGGTGGAAGAATACTGA

Alignment

ORF - retro_mmus_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 88.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTFPDLYRGLTDCCLKTYSQVGFRGFYKGTSPALIANIAENSVLFMCYGFCQQVVRKVVGLDQQAKLSD
          MQTFP.LY.GL.DC.LKTY.QVG.RG.Y.GTSPAL.A.....SVLFMC.GFCQQ.VRKV....Q.A.L.D
Retrocopy MQTFPQLYKGLADCFLKTYNQVGIRGLYRGTSPALLAYVTQGSVLFMCFGFCQQFVRKVARVEQNAELND

Parental  LQNAAAGSFASAFAALVLCPTELVKCRLQTMYEMETSGKIAASQNTVWSVVKEIFRKDGPLGFYHGLSST
          L..A.AGS.ASAFAAL.LCPTELVKCRLQTMYEM..SGKIA.S.NT.WS.VK.IF.KDGPLGFY.GLS.T
Retrocopy LETATAGSLASAFAALALCPTELVKCRLQTMYEMKMSGKIAQSYNTIWSMVKSIFMKDGPLGFYRGLSTT

Parental  LLREVPGYFFFFGGYELSRSFFASGRSKDELGPVPLMLSGGFGGICLWLAVYPVDCIKSRIQVLSMTGKQ
          L..E.PGYFF.FGGYE.SRSFFASG.SKDELGPVPLMLSGGF.GICLWL...PVDCIKSRIQVLSM.GK.
Retrocopy LAQEIPGYFFYFGGYEISRSFFASGGSKDELGPVPLMLSGGFAGICLWLIIFPVDCIKSRIQVLSMFGKP

Parental  TGLVRTFLSIVKNEGITALYSGLKPTMIRAFPANGALFLAYEYSRKLMMNQLEAW
          .GL..TF.S.V.NEGI.ALYSGLK.T.IRA.P.N.ALFL.YEYSRK.MMN..E..
Retrocopy AGLIETFISVVRNEGISALYSGLKATLIRAIPSNAALFLVYEYSRKMMMNMVEEY

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	0.16 RPM	12.22 RPM
SRP007412_cerebellum	0.48 RPM	11.12 RPM
SRP007412_heart	0.09 RPM	14.72 RPM
SRP007412_kidney	0.13 RPM	116.34 RPM
SRP007412_liver	0.22 RPM	329.89 RPM
SRP007412_testis	34.53 RPM	0.64 RPM

ChIP-Seq

RNA Polymerase II activity may be related with retro_mmus_75 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	18:37637695..37638918

EST

No EST(s) were mapped for retro_mmus_75 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_59034	1036 libraries	31 libraries	1 library	2 libraries	2 libraries

The graphical summary, for retro_mmus_75 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_75 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_75 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75 ,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192, retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,