RetrogeneDB ID: retro_mmus_3492

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:100337513..100338665(+)
• Located in intron of: ENSMUSG00000059327

Retrocopy information

• Ensembl ID: ENSMUSG00000080813
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3492
ATGTCCAGCTACACACGGCAGCAGCGGCGGGGTGTGCCCCCACTATCACAGACATGGAGCCGCGTGGTTCCTGACAACTT
TGGCTATGGAAAGGGGAAATGTACTAAACAAGGTCCGTCGGGAGCCCATGAGACGCACTTTGGAGGTGACAAACTTGAAG
ACCTTGAAAAAGCCAATCCATTCTCCTTCAAAGAGTATTTGAAAACCAAGAACCTCAGCCTGTCAAACGAAGACATTACC
ACCAGCCGAATTTACCTGAAGGAAGCCTCAAGGCACCCACTGGGACTAAAGCACAGCTCCCCTGCCTCCAAGCCCATGGG
ATATGGCCTAGATTATCAGCAGCCATTTTGTGAAGACCCAACAAGAGCCAGGAACCTAGAAGAGGATGAAGAAAATGGAT
GGAATAGAACCTACCTGCCACCTGCTCTGGGGCAGACTCATTCCTCTAGAGCCACACAGAACTCGTCACCCCGTGGCACC
TACCTTTCCTTTTTCTCCAACACATCAGAGCTGGCAGGTCCTGAGTCTTTGCCTCCATGGAAGCTGAGCAACACCGACTC
CAGGATCTCTCCAGTATTTCCAGCTGGGATTCCTAATGCAGACTTTGCAGCTCATGAAGACTCCCTAGGGGACAGACACC
TGCGGACGCTGCAAATGAGTTATGAAGCACTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCTAAATGAGGTTCAGAGC
TTCTCTGAAACTCAAAGAGAAATGGTGCGGACGCTCGAATGGAAGTTGGAGGCGAAGATGATCAAGGAGGAGAGTGACTT
CCATGACCTCGAGTCAGCAGTCCAGCAAGTCAAACAGAACCTCGAACTGATGACCAAACGGACTGTAAAAGCAGAAAATC
ATGTCTTGAGGCTGAAGCAGGAAATAAATTTGCTTCAGGCACAGCTCTCAAACTTGAGGCGAGAAAATGAAGCCCTGCAA
TCAGACCAGGATGCCAGCCTTACTGTAGTGAAGCAGAGCATGGATGTGGCCTTGCAGAACCTCAGTGTTGTCATGCACAG
TGCACAGGCATCCATAAAGCAGCTGTTATCTGGAGGAGAGACACTGAACCTTGTTGCTGAACTCCTTAAGTCTATCGACA
AAATTACTGAAGTTAAAGCTGAGGCAGACTCT

Alignment

ORF - retro_mmus_3492 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGYARRQ--GAPPLSRTRSLVVPDGFGYGKGKCTNQGPSGAPETRFGGDKLEDLEEANPFSFKEFLKTK
          MS.Y.R.Q..G.PPLS.T.S.VVPD.FGYGKGKCT.QGPSGA.ET.FGGDKLEDLE.ANPFSFKE.LKTK
Retrocopy MSSYTRQQRRGVPPLSQTWSRVVPDNFGYGKGKCTKQGPSGAHETHFGGDKLEDLEKANPFSFKEYLKTK

Parental  NLSLSKEDTTTSRIYPKEASRHPLGLEHSSPASQLMGYGLESQQPFFEDPTRASNLEEDEDDGWNITYLP
          NLSLS.ED.TTSRIY.KEASRHPLGL.HSSPAS..MGYGL..QQPF.EDPTRA.NLEEDE..GWN.TYLP
Retrocopy NLSLSNEDITTSRIYLKEASRHPLGLKHSSPASKPMGYGLDYQQPFCEDPTRARNLEEDEENGWNRTYLP

Parental  SAVDQTHSSRDTQDSPPCDTYLSFFSNSSELACPESLPPWTLSDTDSRISPASPAGSPNADFAAHEESLG
          .A..QTHSSR.TQ.S.P..TYLSFFSN.SELA.PESLPPW.LS.TDSRISP..PAG.PNADFAAHE.SLG
Retrocopy PALGQTHSSRATQNSSPRGTYLSFFSNTSELAGPESLPPWKLSNTDSRISPVFPAGIPNADFAAHEDSLG

Parental  DRHLRTLQISYEALKDENSKLRRKLNEVQSFSETQTEMVRTLERKLEAKMIKEESDFHDLESVVQQVEQN
          DRHLRTLQ.SYEALKDENSKLRRKLNEVQSFSETQ.EMVRTLE.KLEAKMIKEESDFHDLES.VQQV.QN
Retrocopy DRHLRTLQMSYEALKDENSKLRRKLNEVQSFSETQREMVRTLEWKLEAKMIKEESDFHDLESAVQQVKQN

Parental  LELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRSGQGASLSVVKQNTDVALQNLHLVMNSAHA
          LELMTKR.VKAENHVL.LKQEINLLQAQLSNLRRENEAL.S.Q.ASL.VVKQ..DVALQNL..VM.SA.A
Retrocopy LELMTKRTVKAENHVLRLKQEINLLQAQLSNLRRENEALQSDQDASLTVVKQSMDVALQNLSVVMHSAQA

Parental  SIKQLVSGADTLNLVAEILKSIDRISEVKDEVDS
          SIKQL.SG..TLNLVAE.LKSID.I.EVK.E.DS
Retrocopy SIKQLLSGGETLNLVAELLKSIDKITEVKAEADS

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	0.03 RPM	26.40 RPM
SRP007412_kidney	0.04 RPM	42.23 RPM
SRP007412_liver	0.00 RPM	21.14 RPM
SRP007412_testis	2.20 RPM	161.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3492 was not detected

EST

No EST(s) were mapped for retro_mmus_3492 retrocopy.

TSS

No TSS is located nearby retro_mmus_3492 retrocopy 5' end.

Lab

retro_mmus_3492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3492 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,