RetrogeneDB ID: retro_mmus_1196

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:46027427..46028738(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Senp3
• Ensembl ID: ENSMUSG00000005204
• Aliases: Senp3, AA408656, Smt3ip, Smt3ip1
• Description: SUMO/sentrin specific peptidase 3 [Source:MGI Symbol;Acc:MGI:2158736]

Sequence

>retro_mmus_1196
TGCTCACAGCGGCGGCGCCGGCGCCGAGCCACGAGAGCCTTCCAGATGCTGCTCTACTCAAAAAGCACCTCGCTGACATT
CCACTGGAAGCTTTGGGGGCGCGACCAAGGCCGGTGGCGGAACCTCGCACACCCCAAGAACCAGCTCTCACCCCAGGAAG
GGGGTGCAACGCCACAGGTGCCATCACCCTGCTGTGGTTTTGACTTCCCCAGGGGCTACCCCCACCCCGGCTGGGTCTGC
TAGGTGCTCTCATGGCAGAGGATGGGATGAGAGGGTCTTCACCAGTGCCCTCTGGGCCCCCCATGGAGGAAGATGGACTA
AGGTGGACCCCAAAGTCTCCTCTGGACCCTGACTTGGGCCTCCTCTCATGTACTCTACCTAATGATTTTGGGGGTCTGTC
TGGTCCTGAAGGGGAGCGCAGCCTGGCACCCCCTGATGCCAGCATACTCATCAGTAATGTGTGCAGCATTGGAGACCACG
TGGCTCAGGAACTTTTTCAGAGCTCTGACTTGGGCACTGCAGAAGAGGCAGATCGGACTGGGGAGAAAACTGGCCAGCAT
AGCCCCCTTCGGGAGGAACATGTGACCTGTGTGCAGAGTATCTTAGATGAATTCCTTCAAACTTACGGCAGCCTCATCCC
TCTCAGCACTGATGAAGTTGTAGAGAAGTTGGAGGACGTTTTCCAGCAGGAGTTCTCTACACCCTCATGGAAGAGTCTGG
TACTACAGCTGATCCAGTCTTATCAGCGGATGCCAGACAACGCTATGGTAAGGGGCTTCCGGGTATCCTATAAGTGACAC
GTGCTCACCATGGATGACTTGGGTACCTTATATGGACAGAACTGGCTCAATGACCAGGTGATGAACATGTATGGAGACCT
GGTCATGGACACAGTCCCTGAAAAGGTGCATTTCTTCCACAGTCTCTTCTATGATAAACTCCGTACCAAGGGTTATGATG
GGGTAAAGAGGTGGACCAAAAATGTGGACATCTTCAATAAGGAATTACTGCTAATCCCCATCCATCTGGAAGTGGACTGG
TCCCTTATCTCAGTTGATGTAAGGCAACATACCATCACCTATTTTGACTCCCAGCGAACTCTAAATCGCCGCTGCCCTAA
GTATATTGTCAAGTATCTACAGGCAGAGGCAGTCAAAAAAAGGCCAAGTGGACTTCCATCAGGGCTGGAAAGGTTATTTC
AAAATGAATGTGGCCAGGCAGAATAATGACAGTGACTGTGGTGCCTTTGTGTTACAGTACTGCAAGCACCTGGCCCTGTC
TCAGCCATTCAGCTTCACCCAGCAGGACATC

Alignment

ORF - retro_mmus_1196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 76.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CSQRRRR--AMRAFQMLLYSKSTSLTFHWKLWGRHRGRRRNLAHPKNHLSPQEGGATPQVPSPCCRFDSP
          CSQRRRR..A.RAFQMLLYSKSTSLTFHWKLWGR..GR.RNLAHPKN.LSPQEGGATPQVPSPCC.FD.P
Retrocopy CSQRRRRRRATRAFQMLLYSKSTSLTFHWKLWGRDQGRWRNLAHPKNQLSPQEGGATPQVPSPCCGFDFP

Parental  RG-LPPPRLGLLGALMAEDGMRGSPPVPSGPPMEEDGLRWTPKSPLDPDSGLLSCTLPNGFGGLSGPEGE
          RG.LPPPRLGLLGALMAEDGMRGS.PVPSGPPMEEDGLRWTPKSPLDPD.GLLSCTLPN.FGGLSGPEGE
Retrocopy RG<LPPPRLGLLGALMAEDGMRGSSPVPSGPPMEEDGLRWTPKSPLDPDLGLLSCTLPNDFGGLSGPEGE

Parental  RSLAPPDASILISNVCSIGDHVAQELFQSSDLGIAEEADRTGEKAGQHSPLREEHVTCVQSILDEFLQTY
          RSLAPPDASILISNVCSIGDHVAQELFQSSDLG.AEEADRTGEK.GQHSPLREEHVTCVQSILDEFLQTY
Retrocopy RSLAPPDASILISNVCSIGDHVAQELFQSSDLGTAEEADRTGEKTGQHSPLREEHVTCVQSILDEFLQTY

Parental  GSLIPLSTDEVVEKLEDIFQQEFSTPSRKSLVLQLIQSYQRMPGNAMVRGFRVSYKRHVLTMDDLGTLYG
          GSLIPLSTDEVVEKLED.FQQEFSTPS.KSLVLQLIQSYQRMP.NAMVRGFRVSYK.HVLTMDDLGTLYG
Retrocopy GSLIPLSTDEVVEKLEDVFQQEFSTPSWKSLVLQLIQSYQRMPDNAMVRGFRVSYK*HVLTMDDLGTLYG

Parental  QNWLNDQVMNMYGDLVMDTVPEKVHFFNSFFYDKLRTKGYDGVKRWTKNVDIFNKELLLIPIHLEVHWSL
          QNWLNDQVMNMYGDLVMDTVPEKVHFF.S.FYDKLRTKGYDGVKRWTKNVDIFNKELLLIPIHLEV.WSL
Retrocopy QNWLNDQVMNMYGDLVMDTVPEKVHFFHSLFYDKLRTKGYDGVKRWTKNVDIFNKELLLIPIHLEVDWSL

Parental  ISVDVRRRTITYFDSQRTLNRRCPKHIAKYLQAEAV-KKDRLDFHQGWKGYFKMNVARQNNDSDCGAFVL
          ISVDVR..TITYFDSQRTLNRRCPK.I.KYLQAEAV.KK...DFHQGWKGYFKMNVARQNNDSDCGAFVL
Retrocopy ISVDVRQHTITYFDSQRTLNRRCPKYIVKYLQAEAV>KKGQVDFHQGWKGYFKMNVARQNNDSDCGAFVL

Parental  QYCKHLALSQPFSFTQQDM
          QYCKHLALSQPFSFTQQD.
Retrocopy QYCKHLALSQPFSFTQQDI

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	58.78 RPM
SRP007412_cerebellum	0.00 RPM	66.78 RPM
SRP007412_heart	0.06 RPM	29.98 RPM
SRP007412_kidney	0.04 RPM	40.08 RPM
SRP007412_liver	0.03 RPM	30.53 RPM
SRP007412_testis	0.14 RPM	59.55 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1196 was not detected

EST

No EST(s) were mapped for retro_mmus_1196 retrocopy.

TSS

No TSS is located nearby retro_mmus_1196 retrocopy 5' end.

Lab

retro_mmus_1196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1196 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000131	1 retrocopy	retro_btau_710,
Echinops telfairi	ENSETEG00000006699	2 retrocopies	retro_etel_1251, retro_etel_545,
Mus musculus	ENSMUSG00000005204	1 retrocopy	retro_mmus_1196 ,