RetrogeneDB ID: retro_mmus_1545

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:12356719..12357608(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sdccag3
• Ensembl ID: ENSMUSG00000026927
• Aliases: Sdccag3, C330016H24Rik, C630038K21Rik
• Description: serologically defined colon cancer antigen 3 [Source:MGI Symbol;Acc:MGI:1915362]

Sequence

>retro_mmus_1545
GCCGCAAGGCACCCACTGGGACTAGAGCACAGCTCCCCTGCCTCCCAGCCCCATGGGATATGGCCTGGAATATCAGCAGC
CATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGATGGATGGAATAGAACCTACCTGCCATCTGTC
CTGGGTCAGACTCATTCCTCCTCTAGAGCCACACAGAACTTGTCACCCCGTGGCACCTACCTTTCCTTTTTTTTCCAACG
CGTCAGAGCTGGCAGGTCCCGAGTCTTTGCCCCCATGGACGCTGAGCGACACTGACTGCAGGACCTCCCCAGCATCTCCA
GTTGGGAGTCCTAATGCAGACTTTGCAGCTCATGAAGACTCCTTAGGGGACAGATACCTGCGGACGTTGCAGATAAGTTA
TGGAGCACTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCTAAATGAGGCTCAGAGCTTCTCTGAAACTCAAACAAAAA
TGGTGAGGACGCTCAAATGGAAGTTGGAAGGGAAGATGATCAAGGAGGAGAGTGACTTCCATGACCTCCAGTCAGTAGTC
CAGCAAGTGGAACAGAACCTCTAACTGATGACCAAACGGGCTGTAAGAGCAGAAAATCACGTCTTGAAGCTGAAACAGGA
AAGAAATTCGCTTCAGGCACAGCTCTCAAACTTGTGGTGAGAAAATGCAGCCCTGCAGTCAGGCCAGGTGCTAGCCTCAC
CGTGGTGAAGCAGAACACCGATGTGGCCTTGCAGAACCTCCGTGTTGTCATGCACAGGGCACACTCATCCATAAAGCAGC
TGGCATCTGGGGCAGAGACACTGAACCTTGTTGCTGAACTCCTCAAGTCGATCGACAGAATTACTGAATTTAAAGCTGAG
GCGGGCTCC

Alignment

ORF - retro_mmus_1545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81. %
• Parental protein coverage: 77.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASRHPLGLEHSSPASQL-MGYGLESQQPFFEDPTRASNLEEDEDDGWNITYLPSAVDQTHSS-RDTQDSP
          A.RHPLGLEHSSPASQ..MGYGLE.QQPFFEDPTRASNLEEDED.GWN.TYLPS...QTHSS.R.TQ...
Retrocopy AARHPLGLEHSSPASQP>MGYGLEYQQPFFEDPTRASNLEEDED-GWNRTYLPSVLGQTHSSSRATQNLS

Parental  PCDTYLSFFS-NSSELACPESLPPWTLSDTDSRISPASPAGSPNADFAAHEESLGDRHLRTLQISYEALK
          P..TYLS....N.SELA.PESLPPWTLSDTD.R.SPASP.GSPNADFAAHE.SLGDR.LRTLQISY.ALK
Retrocopy PRGTYLSXXX>NASELAGPESLPPWTLSDTDCRTSPASPVGSPNADFAAHEDSLGDRYLRTLQISYGALK

Parental  DENSKLRRKLNEVQSFSETQTEMVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHV
          DENSKLRRKLNE.QSFSETQT.MVRTL..KLE.KMIKEESDFHDL.SVVQQVEQNL.LMTKRAV.AENHV
Retrocopy DENSKLRRKLNEAQSFSETQTKMVRTLKWKLEGKMIKEESDFHDLQSVVQQVEQNL*LMTKRAVRAENHV

Parental  LKLKQEINLLQAQLSNLRRENEALRSGQ-GASLSVVKQNTDVALQNLHLVMNSAHASIKQLVSGADTLNL
          LKLKQE.N.LQAQLSNL..EN.AL.SGQ.GASL.VVKQNTDVALQNL..VM..AH.SIKQL.SGA.TLNL
Retrocopy LKLKQERNSLQAQLSNLW*ENAALQSGQ<GASLTVVKQNTDVALQNLRVVMHRAHSSIKQLASGAETLNL

Parental  VAEILKSIDRISEVKDEVDS
          VAE.LKSIDRI.E.K.E..S
Retrocopy VAELLKSIDRITEFKAEAGS

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	63.52 RPM
SRP007412_cerebellum	0.00 RPM	80.24 RPM
SRP007412_heart	0.00 RPM	26.40 RPM
SRP007412_kidney	0.04 RPM	42.23 RPM
SRP007412_liver	0.00 RPM	21.14 RPM
SRP007412_testis	0.00 RPM	161.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1545 was not detected

EST

No EST(s) were mapped for retro_mmus_1545 retrocopy.

TSS

No TSS is located nearby retro_mmus_1545 retrocopy 5' end.

Lab

retro_mmus_1545 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1545 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000165689	1 retrocopy	retro_hsap_1944,
Gorilla gorilla	ENSGGOG00000010905	1 retrocopy	retro_ggor_1414,
Mus musculus	ENSMUSG00000026927	3 retrocopies	retro_mmus_1545 , retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys	ENSNLEG00000008186	1 retrocopy	retro_nleu_891,
Otolemur garnettii	ENSOGAG00000015872	1 retrocopy	retro_ogar_3418,
Pongo abelii	ENSPPYG00000019772	2 retrocopies	retro_pabe_1612, retro_pabe_256,
Pan troglodytes	ENSPTRG00000021555	1 retrocopy	retro_ptro_1300,
Rattus norvegicus	ENSRNOG00000018876	2 retrocopies	retro_rnor_1215, retro_rnor_2770,