RetrogeneDB ID: retro_mmus_1227

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:105043449..105044354(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prpf38a
• Ensembl ID: ENSMUSG00000063800
• Aliases: Prpf38a, 2410002M20Rik
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:MGI Symbol;Acc:MGI:1916962]

Sequence

>retro_mmus_1227
AGTGAAGGCATCCATGGCACCATCCCTCAGCATCTGGTGGAGAAGATCATCCAGACACGAATCTATGAATCAAAGTACTG
GAAAGAAGAGTGCTTTGGACTTACAGCTGAACTTGTAGTGGACAAAGCCATGGAGTTAAAATTCGTGGGTGGTGTGTATG
TTGGAAACATAAAGCCAACTCATTTTTTTGTGTTTAATCTTGAAGATGCTTCAAATTCTACCTGAGAAGGATATCATGGT
TGAGTACATAAAAAGTGAAGATTTCAAGTATATCCTCGTGTTGGGGGCACTTTACATGCGGCTGACAGGAACTGCAATTG
ATTGCTACAAGTACTTCGAGCCTTTGTATGGAAAAATCAAGAGCCAGAACCGAAATGGACAGTTTGTACTAATGCATTTA
GACGATTTCATTTATGAACTACTGCACAGTGAGAGAGTCTGTGATATCATTTTGCCCCGGCTACAGAAATGGTATGTGCT
GGAAGAAGCTAAACAACTGGAGCATCGAGTTAGTGCTCTAGAAGAGGACATGGATGACGTGGAGTCTAGTGAGGAAGAGG
AGGAGGAAGATGAGAAGCTGGAAAGAGTGCCATCATCTGACCATCGACGAAGAAGCTACAGAGACTTGGACAAGCCAAGG
CGCTCACTTGCACTGTGCTACCAGAGAAGCCAGAGTGATTCTCCCAGAAGGCAGAGTAGATCCCCTAAAAGAAGAAAGTC
CTTCTCCCCGAAGAGATAGGCATAGGAGCAAGAGTCCATGACACCATCGAAGCAGGTCTAGAGACAGACGACATAGATCC
CACTCTTAATCCCCAGGTCACCACCATAGTCACAGACATAGAAGCCACTCACAGTCTCCTGAAAGGCCAAAGAAAAGCCA
CAAGAAGAGCCGGAGAGGAAATAAG

Alignment

ORF - retro_mmus_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 97.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AHSIHGTNPQYLVEKIIRTRIYESKYWKEECFGLTAELVVDKAMELKFVGGVYGGNIKPTPF-LCLTLKM
          ...IHGT.PQ.LVEKII.TRIYESKYWKEECFGLTAELVVDKAMELKFVGGVY.GNIKPT.F.LCL.LKM
Retrocopy SEGIHGTIPQHLVEKIIQTRIYESKYWKEECFGLTAELVVDKAMELKFVGGVYVGNIKPTHF>LCLILKM

Parental  LQIQPEKDIIVEFIKNEDFKYVRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGEFVLMHVDEF
          LQI.PEKDI.VE.IK.EDFKY...LGALYMRLTGTAIDCYKY.EPL...Y.KIKSQNRNG.FVLMH.D.F
Retrocopy LQILPEKDIMVEYIKSEDFKYILVLGALYMRLTGTAIDCYKYFEPL---YGKIKSQNRNGQFVLMHLDDF

Parental  IYELLHSERVCDIILPRLQKRYVLEEAEQLEPRVSALEEDMDDVESSEEEEEEDEKLERVPSPDHRRRSY
          IYELLHSERVCDIILPRLQK.YVLEEA.QLE.RVSALEEDMDDVESSEEEEEEDEKLERVPS.DHRRRSY
Retrocopy IYELLHSERVCDIILPRLQKWYVLEEAKQLEHRVSALEEDMDDVESSEEEEEEDEKLERVPSSDHRRRSY

Parental  RDLDKPRRSPALRYRRSRSRSPRRRSRSPKRR-SPSPRRERHRSKSPRRHRSRSRDRRHRSRSKSPGHHR
          RDLDKPRRS.AL.Y.RS.S.SPRR.SRSPKRR.SPSPRR.RHRSKSP..HRSRSRDRRHRS.S.SPGHH.
Retrocopy RDLDKPRRSLALCYQRSQSDSPRRQSRSPKRR>SPSPRRDRHRSKSP*HHRSRSRDRRHRSHS*SPGHHH

Parental  SHRHRSHSKSPERSKKSHKKSRRGNE
          SHRHRSHS.SPER.KKSHKKSRRGN.
Retrocopy SHRHRSHSQSPERPKKSHKKSRRGNK

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	17.59 RPM
SRP007412_cerebellum	0.00 RPM	20.71 RPM
SRP007412_heart	0.00 RPM	11.33 RPM
SRP007412_kidney	0.00 RPM	13.76 RPM
SRP007412_liver	0.00 RPM	9.26 RPM
SRP007412_testis	0.05 RPM	32.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1227 was not detected

EST

No EST(s) were mapped for retro_mmus_1227 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_32341	535 libraries	265 libraries	261 libraries	7 libraries	4 libraries

The graphical summary, for retro_mmus_1227 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1227 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227 , retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,