RetrogeneDB ID: retro_mmus_3359

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:78820640..78821840(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000059422
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: 2410127L17Rik
• Ensembl ID: ENSMUSG00000024726
• Aliases: None
• Description: RIKEN cDNA 2410127L17 gene [Source:MGI Symbol;Acc:MGI:1914633]

Sequence

>retro_mmus_3359
ATGCAGCGACGACAGCGCGCTCCGCCCGCGTCTCAACCGGCCCAGGACGGCGGGCGAAGCGAGGACGTGGAGGTGCAGTT
CTCCGCCGGGCGTTTGGGCTCGGCCGCGCCTGCGGGGCCCCCGGCGCGCGGCACCGCGGAGGACGAGGAGCGGCTGGAGC
GCGAGCACTTCTGGAAGGTCATCAACGCGTTCCGCTACTACGGCACCAGCATGCATGAACGAGTGAACAGAACAGAAAGA
CAGTTTCGGTCCCTTCCAGAGAACCAGCAGAAACTGCTTCCTCAGTTTCCTCTTCACTTGGACAAGATCCGGAAATGCAT
TGACCATAATCAGGAAATACTGCTGACCATTGTGAATGATTGCATACATATGTTCGAAAATAAAGAATATGGAGAAGATG
CCAATGGAAAGATTATGCCAGCATCTACATTTGACATGGATAAGTTAAAATCTACACTGAAACAGTTTGTAAGAGACTGG
AGTGAGACCGGGAAAGCAGAAAGGGACGCCTGCTATAAGCCAATCATTAAAGAGATTATCAAAAATTTTCCAAAGGAGAG
ATGGGATCCTTCTAAAGTAAATATTCTGGTACCTGGTGCTGGACTAGGAAGATTGGCCTGGGAAGTAGCTATGCTAGGTT
ATGCTTGTCAAGGAAATGAATGGAGTTTTTTTATGCTCTTTTCTTCCAACTTTGTACTCAACAGATGTTCTGAAATTAAC
AAATATAAACTTTATCCCTGGATCCATCAGTTTAGCAATAATCGGAGATCAGCTGATCAGATCCGACCCATTCTTTTCCC
TGATGTTGACCCCCACAGTCTTCCTCCTGGTTCTAACTTTTCCATGACAGCAGGAGACTTTCAGGAGATTTACTCTGAAT
GCAATGCCTGGGACTGTATTGCCACCTGCTTCTTCATAGACACAGCTCACAATGTAATTGATTATATTGATACAATATGG
AGAATACTCAAGCCAGGTGGAATCTGGATAAATCTTGGTCCTCTACTATACCATTTTGAAAATCTGGCAAATGAACTGTC
TATAGAATTGAGCTATGAGGATATTAAAAATGTTGTTCTTCAGTATGGATTTCAGCTAGAGGTGGAGAAAGAATCTGTAT
TGTCAACATATACTGTGAATGATCTCTCTATGATGAAATACTACTATGAGTGTGTTTTGTTTGTGGTCCGGAAGCCACAA

Alignment

ORF - retro_mmus_3359 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQRRQRAPPASQPAQDGGRSEDVEVQFSAGRLGSAAPAGPPARGTAEDEERLEREHFWKVINAFRYYGTS
          MQRRQRAPPASQPAQDGGRSEDVEVQFSAGRLGSAAPAGPPARGTAEDEERLEREHFWKVINAFRYYGTS
Retrocopy MQRRQRAPPASQPAQDGGRSEDVEVQFSAGRLGSAAPAGPPARGTAEDEERLEREHFWKVINAFRYYGTS

Parental  MHERVNRTERQFRSLPENQQKLLPQFPLHLDKIRKCIDHNQEILLTIVNDCIHMFENKEYGEDANGKIMP
          MHERVNRTERQFRSLPENQQKLLPQFPLHLDKIRKCIDHNQEILLTIVNDCIHMFENKEYGEDANGKIMP
Retrocopy MHERVNRTERQFRSLPENQQKLLPQFPLHLDKIRKCIDHNQEILLTIVNDCIHMFENKEYGEDANGKIMP

Parental  ASTFDMDKLKSTLKQFVRDWSETGKAERDACYKPIIKEIIKNFPKERWDPSKVNILVPGAGLGRLAWEVA
          ASTFDMDKLKSTLKQFVRDWSETGKAERDACYKPIIKEIIKNFPKERWDPSKVNILVPGAGLGRLAWEVA
Retrocopy ASTFDMDKLKSTLKQFVRDWSETGKAERDACYKPIIKEIIKNFPKERWDPSKVNILVPGAGLGRLAWEVA

Parental  MLGYACQGNEWSFFMLFSSNFVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPILFPDVDPHSLPPGSNF
          MLGYACQGNEWSFFMLFSSNFVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPILFPDVDPHSLPPGSNF
Retrocopy MLGYACQGNEWSFFMLFSSNFVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPILFPDVDPHSLPPGSNF

Parental  SMTAGDFQEIYSECNAWDCIATCFFIDTAHNVIDYIDTIWRILKPGGIWINLGPLLYHFENLANELSIEL
          SMTAGDFQEIYSECNAWDCIATCFFIDTAHNVIDYIDTIWRILKPGGIWINLGPLLYHFENLANELSIEL
Retrocopy SMTAGDFQEIYSECNAWDCIATCFFIDTAHNVIDYIDTIWRILKPGGIWINLGPLLYHFENLANELSIEL

Parental  SYEDIKNVVLQYGFQLEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ
          SYEDIKNVVLQYGFQLEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ
Retrocopy SYEDIKNVVLQYGFQLEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ

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	0.05 RPM	0.65 RPM
SRP007412_cerebellum	0.09 RPM	0.83 RPM
SRP007412_heart	0.03 RPM	3.74 RPM
SRP007412_kidney	0.15 RPM	1.77 RPM
SRP007412_liver	0.14 RPM	1.09 RPM
SRP007412_testis	0.18 RPM	2.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3359 was not detected

EST

No EST(s) were mapped for retro_mmus_3359 retrocopy.

TSS

No TSS is located nearby retro_mmus_3359 retrocopy 5' end.

Lab

retro_mmus_3359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3359 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024726	2 retrocopies	retro_mmus_1013, retro_mmus_3359 ,
Oryctolagus cuniculus	ENSOCUG00000017017	4 retrocopies	retro_ocun_1659, retro_ocun_1737, retro_ocun_1827, retro_ocun_921,
Ictidomys tridecemlineatus	ENSSTOG00000000385	5 retrocopies	retro_itri_1389, retro_itri_1652, retro_itri_1653, retro_itri_1654, retro_itri_1843,