RetrogeneDB ID: retro_mmus_1289

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:70723220..70723409(-)
• Located in intron of: ENSMUSG00000022100

Retrocopy information

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

Parental gene information

• Parental gene symbol: 2810417H13Rik
• Ensembl ID: ENSMUSG00000040204
• Aliases: 2810417H13Rik, AA409629, Ns5apt9, Ns5atp9, PAF15, Paf, mKIAA0101, p15(PAF)
• Description: RIKEN cDNA 2810417H13 gene [Source:MGI Symbol;Acc:MGI:1915276]

Sequence

>retro_mmus_1289
ATGGTGCGGACCAAAGCAAACTACGTCCCAGGAGCCTACAGAAAAGCGCTGGCTTCTCAAGCCCCTAGGAAGGTGCCTGG
CTCCTCCACCTTTGTCACCAGTTCTTCAAGTTCATCGAGAAAAGCTGAAAATAAGTATGCAGGAGGGAACCCAGTCTGTG
TGCGCCCAACTCCCAAAAAGGCATCGGGG

Alignment

ORF - retro_mmus_1289 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 57.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVRTKANYVPGAYRKAVASQAPRKVLGSSTFVTNSSSSSRKAENKYAGGNPVCVRPTPKWQKG
          MVRTKANYVPGAYRKA.ASQAPRKV.GSSTFVT.SSSSSRKAENKYAGGNPVCVRPTPK...G
Retrocopy MVRTKANYVPGAYRKALASQAPRKVPGSSTFVTSSSSSSRKAENKYAGGNPVCVRPTPKKASG

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	0.68 RPM
SRP007412_cerebellum	0.04 RPM	0.52 RPM
SRP007412_heart	0.09 RPM	0.25 RPM
SRP007412_kidney	0.04 RPM	1.04 RPM
SRP007412_liver	0.03 RPM	0.44 RPM
SRP007412_testis	0.00 RPM	3.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1289 was not detected

EST

No EST(s) were mapped for retro_mmus_1289 retrocopy.

TSS

No TSS is located nearby retro_mmus_1289 retrocopy 5' end.

Lab

• Experiment type: PCR amplification
• Forward primer: AGCAAAGACCGTAGAGTAGCAAG (23 nt long)
• Reverse primer: ATGTCAGATACATTCTCCCTAGCTT (25 nt long)
• Anneling temperature: 57 °C
• (Expected) product size: 726
• Electrophoresis gel image:
• Additional comment: Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010763	2 retrocopies	retro_chof_1104, retro_chof_892,
Cavia porcellus	ENSCPOG00000006482	3 retrocopies	retro_cpor_138, retro_cpor_186, retro_cpor_365,
Dipodomys ordii	ENSDORG00000014912	1 retrocopy	retro_dord_674,
Monodelphis domestica	ENSMODG00000027710	2 retrocopies	retro_mdom_1275, retro_mdom_776,
Mus musculus	ENSMUSG00000040204	7 retrocopies	retro_mmus_1088, retro_mmus_1289 , retro_mmus_1335, retro_mmus_1844, retro_mmus_2809, retro_mmus_2964, retro_mmus_378,
Otolemur garnettii	ENSOGAG00000003982	1 retrocopy	retro_ogar_501,
Rattus norvegicus	ENSRNOG00000016561	5 retrocopies	retro_rnor_1162, retro_rnor_1412, retro_rnor_2595, retro_rnor_2624, retro_rnor_2698,
Ictidomys tridecemlineatus	ENSSTOG00000019643	4 retrocopies	retro_itri_1241, retro_itri_1324, retro_itri_1888, retro_itri_929,
Tupaia belangeri	ENSTBEG00000013732	2 retrocopies	retro_tbel_3099, retro_tbel_4093,