RetrogeneDB ID: retro_mmus_3389

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: GL456366.1:27162..27975(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Eri1
• Ensembl ID: ENSMUSG00000031527
• Aliases: Eri1, 3'hexo, 3110010F15Rik, Thex1, eri-1
• Description: exoribonuclease 1 [Source:MGI Symbol;Acc:MGI:1914526]

Sequence

>retro_mmus_3389
GGGCCAGGAGCATGGCGGCGGGGCGCAGCAGAAGACTCCGAGGAGTCCCAGCCGCTGAGCATGGAGGAAAAGCAGGGATG
CAGATGTGATGGCAAAGAGACAGACGGATCGAAGTTCATTTCCTCCAATGGCAGTGACTTCAGTGACCCGGTTTACAAAG
AGATCGCTATGACAAATGGTTGTATCAACCAAATGAGTAAGGAGGAACTCAGAGCTAAACTTTCAGAATTTAAGCTTGAA
ACAAGAGGAGTCAAGGATGTTCTAAAGAAGAGACTGAAAAACTATTACAGGAAGCAGAAGTTGATGCTGAAAGAGAGCTC
TGCTGTGGACAGTTACTATGACTACATTTGTATTATTGACTTTGAGGCACTTTGTAAAGAGGGGAACCCAGCTGAGTTTC
TACATGAAATCATTGAGTTTCCTGTTGTTCTGTTGAATACACACACCTTAGAAATTGAAGATACATTTCAGCAGTATGTG
AGGCCAGAGGTCAATGCTCAGTTTTCAGAGTTCTGCATCGGTCTTACTGGAATCACTTAGGATCAGGTAGACAGAGCCGA
TGCTTTCCCTCAGGTCCTGAAAAAAGTGATTGAGTGGATGAAGTCAAAGGAGTTGGGAACTAAGTACAAGTACTGCATAC
TAACTGATGGATCCTGGGATATGAGTAAATTCTTAAACATCCAGTGCCAGCTCAGCAGACTCAAATACTCTTCCTTTGCT
AAAAAGTGGATCAATATTCGAAAGTCATACAGAAACTTTTCTAAGGTTCCCAGAAGCCAGACCAAACTAACAATAATGCT
TGAAAAATTAGGA

Alignment

ORF - retro_mmus_3389 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.56 %
• Parental protein coverage: 78.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDAAQQKTPRPECEESRPLSVEKKQRCRLDGKETDGSKFISSNGSDFSDPVYKEIAMTNGCINRMSKEEL
          G..A.........EES.PLS.E.KQ.CR.DGKETDGSKFISSNGSDFSDPVYKEIAMTNGCIN.MSKEEL
Retrocopy GPGAWRRGAAEDSEESQPLSMEEKQGCRCDGKETDGSKFISSNGSDFSDPVYKEIAMTNGCINQMSKEEL

Parental  RAKLSEFKLETRGVKDVLKKRLKNYYKKQKLMLKESSAGDSYYDYICIIDFEATCEEGNPAEFLHEIIEF
          RAKLSEFKLETRGVKDVLKKRLKNYY.KQKLMLKESSA.DSYYDYICIIDFEA.C.EGNPAEFLHEIIEF
Retrocopy RAKLSEFKLETRGVKDVLKKRLKNYYRKQKLMLKESSAVDSYYDYICIIDFEALCKEGNPAEFLHEIIEF

Parental  PVVLLNTHTLEIEDTFQQYVRPEVNDQLSEFCIGLTGITQDQVDRADAFPQVLKKVIEWMKSKELGTKYK
          PVVLLNTHTLEIEDTFQQYVRPEVN.Q.SEFCIGLTGIT.DQVDRADAFPQVLKKVIEWMKSKELGTKYK
Retrocopy PVVLLNTHTLEIEDTFQQYVRPEVNAQFSEFCIGLTGIT*DQVDRADAFPQVLKKVIEWMKSKELGTKYK

Parental  YCILTDGSWDMSKFLSIQCRLSRLKHPAFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKLG
          YCILTDGSWDMSKFL.IQC.LSRLK...FAKKWINIRKSY.NF.KVPRSQTKLTIMLEKLG
Retrocopy YCILTDGSWDMSKFLNIQCQLSRLKYSSFAKKWINIRKSYRNFSKVPRSQTKLTIMLEKLG

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	12.08 RPM
SRP007412_cerebellum	0.04 RPM	14.33 RPM
SRP007412_heart	0.00 RPM	10.24 RPM
SRP007412_kidney	0.04 RPM	12.59 RPM
SRP007412_liver	0.00 RPM	8.66 RPM
SRP007412_testis	0.05 RPM	7.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3389 was not detected

EST

No EST(s) were mapped for retro_mmus_3389 retrocopy.

TSS

No TSS is located nearby retro_mmus_3389 retrocopy 5' end.

Lab

retro_mmus_3389 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3389 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000012988	1 retrocopy	retro_mmur_472,
Mus musculus	ENSMUSG00000031527	1 retrocopy	retro_mmus_3389 ,