RetrogeneDB ID: retro_mmus_723

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:72834119..72835383(+)
• Located in intron of: ENSMUSG00000055670

Retrocopy information

• Ensembl ID: ENSMUSG00000084329
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Srpr
• Ensembl ID: ENSMUSG00000032042
• Aliases: Srpr, 1300011P19Rik, D11Mgi27
• Description: signal recognition particle receptor ('docking protein') [Source:MGI Symbol;Acc:MGI:1914648]

Sequence

>retro_mmus_723
TTCATTCTGAAGCATGGGAAGGGTCTGCACAAATCCAGTAAATCTACAAAGTCGGATACTCCAAAGGAGAAGGGCAAAAA
AGCACCCCGGGTGTGGGAACTAGGTGGCTGTGCTAACAAGGAAGTCTTGGATTACAGTACTCCCACCACCAATGGAACTC
CAGAGGCAGCCTTTTCTGAAGATGTCAACTTGATTTGAGGAACTGGGCCTGGGGGACAGCTTCAAGATCTGGATTGCAGC
AGCTCAGATGATGAAGGGGCCACTCAAAATACCAAGCCTAGTGCTACCAAGGGAACTCGGGGTGGCATGTTTGGGATGCT
GAAGGGTCTGGTGGGTTCCAAGAGCTTGAGTTGAGAAGACATGGAATTTGTGCTAGACAAGATGCGTGATCATCTCATTG
CTAAGAATGTGGCTGCTGACATTGCTGTCCAGCTCTGTGAATCTGTTGCCAGCAAGTTAGAAGGGAAAGTGATGGGGACA
TTTAGCACTGTGACTTCAACAGTCAAGCAAGCTCTACAGGAATTTCTAGTACAGATCCTACAGCTACAGCATCGTGTAGA
CATGCTCTGGGATATCATGGATGCCCAACGTCGCCAGTGCCCTTATGTTGTTACCTTCTGTGGTGTTAATGGAGTAGGGA
AGTCTACCAATCTTGCCAAGATTTCCTTTTGGCTTTTAGAGAATGGCTTTAGTGTCCTCATTGTTGCCTGTGATACATTT
CGGGCTGGGGCTGTTGAGCAGCTTCTTACACACACCCGGCGCCTGACTGCCCTCTATCCCCCCGAGAAGCATGATGGCCA
TACATACAATGCAGTTGCTTGAAAAAGGCTATGGCAAGGACGCTGCTGGCATTGCCATGGCAGCCATTGCCTTTGCACGT
AACCAAGGCTTTGATGTGGTGCTGGTAGACACTGCTGGCCGCATGCAAGACAATGCCCCTCTGATGACTGCCCTGGCCAA
ACTCATTACTGTCAATACACCTGACTTGGTGCTGTTTGTAGGGGAGGCCTTAGTAGGCAACGAAGCTGTGGATCAACTGG
TCAAGTTCAACAGAGCCTTGGCTGACCATTCTATGGCTCAGGCACCTCGGCTCATTGATGGCATTGTTCTTACCAAATTT
GACACCATTGATGGCAAGGTGGGAGCTGCTATCTCTATGACATACATCACAAGCAAACCCATCGTCTTTGTGGGTACTGG
CCAGACCTACTGTGACCTATGCAGTCTCAATGCCAAGGCTGTGGTGGCTGCCCTCATGAAGGCT

Alignment

ORF - retro_mmus_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.6 %
• Parental protein coverage: 66.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FIQKHGKGLDKSSKSTKSDTPKEKGKKAPRVWELGGCANKEVLDYSTPTTNGTPEAALSEDINLIRGTGP
          FI.KHGKGL.KSSKSTKSDTPKEKGKKAPRVWELGGCANKEVLDYSTPTTNGTPEAA.SED.NLI.GTGP
Retrocopy FILKHGKGLHKSSKSTKSDTPKEKGKKAPRVWELGGCANKEVLDYSTPTTNGTPEAAFSEDVNLI*GTGP

Parental  GGQLQDLDCSSSDDEGATQNTKPSATKGTLGGMFGMLKGLVGSKSLSREDMESVLDKMRDHLIAKNVAAD
          GGQLQDLDCSSSDDEGATQNTKPSATKGT.GGMFGMLKGLVGSKSLS.EDME.VLDKMRDHLIAKNVAAD
Retrocopy GGQLQDLDCSSSDDEGATQNTKPSATKGTRGGMFGMLKGLVGSKSLS*EDMEFVLDKMRDHLIAKNVAAD

Parental  IAVQLCESVANKLEGKVMGTFSTVTSTVKQALQESLVQILQPQRRVDMLRDIMDAQRRQRPYVVTFCGVN
          IAVQLCESVA.KLEGKVMGTFSTVTSTVKQALQE.LVQILQ.Q.RVDML.DIMDAQRRQ.PYVVTFCGVN
Retrocopy IAVQLCESVASKLEGKVMGTFSTVTSTVKQALQEFLVQILQLQHRVDMLWDIMDAQRRQCPYVVTFCGVN

Parental  GVGKSTNLAKISFWLLENGFSVLIAACDTFRAGAVEQLRTHTRRLTALHPPEKHGGRT-MVQLFEKGYGK
          GVGKSTNLAKISFWLLENGFSVLI.ACDTFRAGAVEQL.THTRRLTAL.PPEKH.G.T...QL.EKGYGK
Retrocopy GVGKSTNLAKISFWLLENGFSVLIVACDTFRAGAVEQLLTHTRRLTALYPPEKHDGHT>TMQLLEKGYGK

Parental  DAAGIAMEAIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLITVNTPDLVLFVGEALVGNEAVDQLVKF
          DAAGIAM.AIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLITVNTPDLVLFVGEALVGNEAVDQLVKF
Retrocopy DAAGIAMAAIAFARNQGFDVVLVDTAGRMQDNAPLMTALAKLITVNTPDLVLFVGEALVGNEAVDQLVKF

Parental  NRALADHSMAQTPRLIDGIVLTKFDTIDDKVGAAISMTYITSKPIVFVGTGQTYCDLRSLNAKAVVAALM
          NRALADHSMAQ.PRLIDGIVLTKFDTID.KVGAAISMTYITSKPIVFVGTGQTYCDL.SLNAKAVVAALM
Retrocopy NRALADHSMAQAPRLIDGIVLTKFDTIDGKVGAAISMTYITSKPIVFVGTGQTYCDLCSLNAKAVVAALM

Parental  KA
          KA
Retrocopy KA

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	0.23 RPM	51.49 RPM
SRP007412_cerebellum	0.39 RPM	56.36 RPM
SRP007412_heart	0.19 RPM	94.48 RPM
SRP007412_kidney	0.64 RPM	113.01 RPM
SRP007412_liver	0.85 RPM	184.55 RPM
SRP007412_testis	0.41 RPM	59.87 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_723 was not detected

EST

No EST(s) were mapped for retro_mmus_723 retrocopy.

TSS

No TSS is located nearby retro_mmus_723 retrocopy 5' end.

Lab

retro_mmus_723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000011274	1 retrocopy	retro_fcat_775,
Monodelphis domestica	ENSMODG00000004576	1 retrocopy	retro_mdom_1093,
Mus musculus	ENSMUSG00000032042	1 retrocopy	retro_mmus_723 ,