RetrogeneDB ID: retro_mmus_1013

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:61665939..61667140(+)
• Located in intron of: None

Retrocopy information

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

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_1013
ATGCAGCGACGACAGCGCGCTCCGCCCGCGTCTCAACCGGCCCAGGACGGCAGGCGAAGCGAGGACATGGAGGTGCAGTT
CTCCGCCGGGCGTTTGGGCTCGGCCGCGCCTGCCTGGCCCCCCGGCGCGCGGCACCGCGGAGGACGAGGAGCAGCTGGAG
CGGGAGCACTTCTGGAAGGTCATCAATGCTTTCCGCTACTATGGCACCAGCATGCACGAACGAGTGAACAGAACAGAAAG
ACAGTTTCGATCACTTCCAGATAACCAGCAGAAACTGCTTCCTCAGTTTCCTCTTCACTTGGACAAGATCCGGAAATGCA
TTGACCATAATCAGGAAATACTGCTGACCATTGTGAATGATTGCATACATATGTTCGAAAATAAAGAATATGGAGAAGAT
GCCAATGGAAAGATTATGCCAGCATCTACATTTGACATGGATAAGTTAAAATCTACACTGAAACAGTTTGTAAGAGACTG
GAGTGAGACCGGGAAAGCAGAAAGGGACGCCTGCTATAAGCCAATCATTAAAGAGATTATCAAAATTTTTCCAAAAGAGA
GATGGGATCCTTCTAAAGTAAATATTCTGGTACCTGGTGCTGGACTAGGAAGATTGGCCTGGGAAGTAGCTATGCTAGGT
TATGCTTGTCAAGGAAATGAATGGAGTTTTTTTATGCTCTTTTCTTCCAACGTTGTACTCAACAGATGTTCTGAAATTAA
CAAATATAAACTTTATCCCTGGATCCATCAGTTTAGCAATAATCGGAGATCAGCTGATCAGATCCGACCCATTCTTTTCC
CTGATGTTGACCCCCACAGTCGTCCTCCTGATTCTAACTTTTCGATGACAGCAGGAGACTTTCAGGAGATTTACTCCGAA
TGCAGTGCCTGGGACGGTATTGCCACCTGTTTCTTCATAGACACAGCTCACAATGTAAATGATTATATTGATACGTTATG
GAGAATACTCAAGCCACGTGGAATCTGGATAAATCTTGGTCCTCTACTATACCATTTTGAAAATCTGGCAAATGAACTAT
CTATAGAATTGAGCTATGAGGATATTAAAAATGTTGTTCTGCAGTATGGATTTCAGCTAGAGGTGGAGAAAGAATCTGTA
TTGTCAACATATACTGTGAATGATCTCTCTATGATGAAATACTACTATGAGTGTGTTTTGTTTGTGGTCCGAAAGCCACA
A

Alignment

ORF - retro_mmus_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQRRQRAPPASQPAQDGGRSEDVEVQFSAGRLGSAAPA-GPPARGTAEDEERLEREHFWKVINAFRYYGT
          MQRRQRAPPASQPAQDG.RSED.EVQFSAGRLGSAAPA.GPPARGTAEDEE.LEREHFWKVINAFRYYGT
Retrocopy MQRRQRAPPASQPAQDGRRSEDMEVQFSAGRLGSAAPA>GPPARGTAEDEEQLEREHFWKVINAFRYYGT

Parental  SMHERVNRTERQFRSLPENQQKLLPQFPLHLDKIRKCIDHNQEILLTIVNDCIHMFENKEYGEDANGKIM
          SMHERVNRTERQFRSLP.NQQKLLPQFPLHLDKIRKCIDHNQEILLTIVNDCIHMFENKEYGEDANGKIM
Retrocopy SMHERVNRTERQFRSLPDNQQKLLPQFPLHLDKIRKCIDHNQEILLTIVNDCIHMFENKEYGEDANGKIM

Parental  PASTFDMDKLKSTLKQFVRDWSETGKAERDACYKPIIKEIIKNFPKERWDPSKVNILVPGAGLGRLAWEV
          PASTFDMDKLKSTLKQFVRDWSETGKAERDACYKPIIKEIIK.FPKERWDPSKVNILVPGAGLGRLAWEV
Retrocopy PASTFDMDKLKSTLKQFVRDWSETGKAERDACYKPIIKEIIKIFPKERWDPSKVNILVPGAGLGRLAWEV

Parental  AMLGYACQGNEWSFFMLFSSNFVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPILFPDVDPHSLPPGSN
          AMLGYACQGNEWSFFMLFSSN.VLNRCSEINKYKLYPWIHQFSNNRRSADQIRPILFPDVDPHS.PP.SN
Retrocopy AMLGYACQGNEWSFFMLFSSNVVLNRCSEINKYKLYPWIHQFSNNRRSADQIRPILFPDVDPHSRPPDSN

Parental  FSMTAGDFQEIYSECNAWDCIATCFFIDTAHNVIDYIDTIWRILKPGGIWINLGPLLYHFENLANELSIE
          FSMTAGDFQEIYSEC.AWD.IATCFFIDTAHNV.DYIDT.WRILKP.GIWINLGPLLYHFENLANELSIE
Retrocopy FSMTAGDFQEIYSECSAWDGIATCFFIDTAHNVNDYIDTLWRILKPRGIWINLGPLLYHFENLANELSIE

Parental  LSYEDIKNVVLQYGFQLEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ
          LSYEDIKNVVLQYGFQLEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ
Retrocopy LSYEDIKNVVLQYGFQLEVEKESVLSTYTVNDLSMMKYYYECVLFVVRKPQ

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	0.00 RPM	0.83 RPM
SRP007412_heart	0.19 RPM	3.74 RPM
SRP007412_kidney	0.02 RPM	1.77 RPM
SRP007412_liver	0.00 RPM	1.09 RPM
SRP007412_testis	0.05 RPM	2.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1013 was not detected

EST

No EST(s) were mapped for retro_mmus_1013 retrocopy.

TSS

No TSS is located nearby retro_mmus_1013 retrocopy 5' end.

Lab

retro_mmus_1013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1013 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,