RetrogeneDB ID: retro_mmus_711

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:54158925..54160033(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000036045
• 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_711
ATGTCGGGCTACATGCGACAGCAGGGTGCGCCCCCATTATCACGGACTAGGAACCTTGTGGTTCCCGACGATTTTGGCTA
TGGAAAGGGGAAATGTAATAAACAAGGTCCGTCGGGAGCCCATGAGACACGCTTTGGAGGTGACAAACTTGAAGAACTTG
AAGAAGACAATCCATTTTCCTTCAAAGAGTTTTTGAAAGTCAAGAACCTCAGCCTGTCAAAAGAAGACACGACCACCAGC
TGAATTTACCCACAGGAAGCCTTAAGGCACCCACTGGGACTTGAGCACAGCTCCCCTGCCTCCCAGCCCATGGGATATGG
CCTGGAATATCAGCAGCCATTTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGAAGATGGATGGAAT
AGAACCTACCTGCCATCTGTCCTGGTCAGACTCATTCCTCTAGAGCCGCACAGAACTTGTCACCCTGTGGCATCTACCTT
TCCTTTTTCTAAAACGCATCAGAGCTGGCAGGTCCCCAGTCTTTGCCTCCATGGACGCTGAGCAACACTGACTCCAGGAC
CTCCCCAGCAACTCCAGCTGGGAGTCCTAATGCAGACTTTGCAGCTCATGAAGACTCCCTAGGGGACAGACACCTGCGGA
CGCTGCAGATAAGTTATGAAGCACTGAAAGATGAAAACTCTAAGCTCGGAAGAAAGCTAAATGAGGTTCCGAGCTTCTCG
GAAGCTCAAACAGAAATGGTGAGGATACTGTAATGGAAGTTGGAGGCGAAGATGATCAAGGAGGAGAGTGACTTCCATGA
CCTCGAGTCAGCAATCCAGCAAGTCGAACAGAACCTCAAACTGATGACCAAACGGGCCGTAAAAGCAGGAAATCATGTCT
TGAAGCTGAAACAGGAAATAAATTTGCTTCAGGCACAGCTCTCAAACTTCAGGCGGGAAAATGAAGCCCTGCAGTCAGGC
CAGGGTGCCAGCCTCACCGATGTGGCCTTGCAGAACCTCCATGTTGTCATGCACAGGGCACAGGCATCCATAAAGCAGCT
GGCATCTGGGGCAGAGACACTGAACCTTGTTGCTGAACTCCTCAAGTCTATCAACAGAATTACTGAAG

Alignment

ORF - retro_mmus_711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.08 %
• Parental protein coverage: 96.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGYARRQGAPPLSRTRSLVVPDGFGYGKGKCTNQGPSGAPETRFGGDKLEDLEEANPFSFKEFLKTKNL
          MSGY.R.QGAPPLSRTR.LVVPD.FGYGKGKC..QGPSGA.ETRFGGD........NPFSFKEFLK.KNL
Retrocopy MSGYMRQQGAPPLSRTRNLVVPDDFGYGKGKCNKQGPSGAHETRFGGDXXXXXXXDNPFSFKEFLKVKNL

Parental  SLSKEDTTTSRIYPKEASRHPLGLEHSSPASQLMGYGLESQQP-FFEDPTRASNLEEDEDDGWNITYLPS
          SLSKEDTTTS.IYP.EA.RHPLGLEHSSPASQ.MGYGLE.QQP.FFEDPTRASNLEEDE.DGWN.TYLPS
Retrocopy SLSKEDTTTS*IYPQEALRHPLGLEHSSPASQPMGYGLEYQQP>FFEDPTRASNLEEDEEDGWNRTYLPS

Parental  AV-DQTHSSRDTQDSPPCDTYLSFFSNSSELACPESLPPWTLSDTDSRISPASPAGSPNADFAAHEESLG
          ....QTHSSR..Q...PC..YLSFF.N.SELA.P.SLPPWTLS.TDSR.SPA.PAGSPNADFAAHE.SLG
Retrocopy VL<GQTHSSRAAQNLSPCGIYLSFF*NASELAGPQSLPPWTLSNTDSRTSPATPAGSPNADFAAHEDSLG

Parental  DRHLRTLQISYEALKDENSKLRRKLNEVQSFSETQTEMVRTLERKLEAKMIKEESDFHDLESVVQQVEQN
          DRHLRTLQISYEALKDENSKL.RKLNEV.SFSE.QTEMVR.L..KLEAKMIKEESDFHDLES..QQVEQN
Retrocopy DRHLRTLQISYEALKDENSKLGRKLNEVPSFSEAQTEMVRIL*WKLEAKMIKEESDFHDLESAIQQVEQN

Parental  LELMTKRAVKAENHVLKLKQEINLLQAQLSNLRRENEALRSGQGASLS-VVKQNTDVALQNLHLVMNSAH
          L.LMTKRAVKA.NHVLKLKQEINLLQAQLSN.RRENEAL.SGQGASL..V..QN..V.............
Retrocopy LKLMTKRAVKAGNHVLKLKQEINLLQAQLSNFRRENEALQSGQGASLTDVALQNLHVVMHRAQASIKQLA

Parental  ASIKQLVSGADTL-NLVAEILK
          .....L...A..L..L..E.LK
Retrocopy SGAETLNLVAELL>SLSTELLK

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	0.04 RPM	80.24 RPM
SRP007412_heart	0.09 RPM	26.40 RPM
SRP007412_kidney	0.04 RPM	42.23 RPM
SRP007412_liver	0.00 RPM	21.14 RPM
SRP007412_testis	0.27 RPM	161.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_711 was not detected

EST

No EST(s) were mapped for retro_mmus_711 retrocopy.

TSS

No TSS is located nearby retro_mmus_711 retrocopy 5' end.

Lab

retro_mmus_711 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_711 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,