RetrogeneDB ID: retro_mmus_943

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:60423410..60423831(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pigx
• Ensembl ID: ENSMUSG00000023791
• Aliases: Pigx, 2010319C14Rik, PIG-X
• Description: phosphatidylinositol glycan anchor biosynthesis, class X [Source:MGI Symbol;Acc:MGI:1919334]

Sequence

>retro_mmus_943
GAAGGTTTTAACTATTGGTCCAAAGAATTTGCAAATCTCACTTATGCCCAACAGGATGCACAGTGCATCAACTGCTTCTA
GCCCTTTTTACCTGTGAATGATCACTATCACCAGCCACACAGAAAAGATGGTGATACCCTCTTTGTGGTCAACAACCCTG
ACTTACTATACTGAACTGTGACCAGAGTTCCCAATTTTGAAATGCTGGGCTCAGTTAGAAATAGCAGCTCCTTGTGCTTT
GAAAAATGAGGAGATATGTCAGTGGAAAAACAAGCAGTACAAATCAATATTTAAGAATTTGACAGTACAGGCTCCAATGG
GACTGATTATACATACCTCTTTAGTGTGTTCTATGGTACCATTCAATGCAATTCTGTGTTCTACTTTGATCCTTTTATCT
GTTTTCAAATATGGCCATTTT

Alignment

ORF - retro_mmus_943 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.92 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EAPNYLSNESAVLIYARQDAQCIDCFQAFLPVHYRYHRPHKKDGDTLIVVNNPDLLMYCDQEFP-ILKCW
          E..NY.S.E.A.L.YA.QDAQCI.CF..FLPV...YH.PH.KDGDTL.VVNNPDLL.......P.ILKCW
Retrocopy EGFNYWSKEFANLTYAQQDAQCINCF*PFLPVNDHYHQPHRKDGDTLFVVNNPDLLY*TVTRVP>ILKCW

Parental  AQSEVAAPCALKSEEICQWKSMQYKSILKNLTVQVPVGLTIHTSLVCSVTLLITILCSTLILLAVFKYGH
          AQ.E.AAPCALK.EEICQWK..QYKSI.KNLTVQ.P.GL.IHTSLVCS......ILCSTLILL.VFKYGH
Retrocopy AQLEIAAPCALKNEEICQWKNKQYKSIFKNLTVQAPMGLIIHTSLVCSMVPFNAILCSTLILLSVFKYGH

Parental  F
          F
Retrocopy F

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	7.36 RPM
SRP007412_cerebellum	0.00 RPM	5.08 RPM
SRP007412_heart	0.00 RPM	5.54 RPM
SRP007412_kidney	0.00 RPM	9.41 RPM
SRP007412_liver	0.00 RPM	6.72 RPM
SRP007412_testis	0.00 RPM	1.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_943 was not detected

EST

No EST(s) were mapped for retro_mmus_943 retrocopy.

TSS

No TSS is located nearby retro_mmus_943 retrocopy 5' end.

Lab

retro_mmus_943 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_943 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003759	1 retrocopy	retro_amel_386,
Callithrix jacchus	ENSCJAG00000013676	1 retrocopy	retro_cjac_2794,
Monodelphis domestica	ENSMODG00000018455	1 retrocopy	retro_mdom_1758,
Mustela putorius furo	ENSMPUG00000003841	1 retrocopy	retro_mputfur_1090,
Mus musculus	ENSMUSG00000023791	1 retrocopy	retro_mmus_943 ,
Oryctolagus cuniculus	ENSOCUG00000012329	1 retrocopy	retro_ocun_977,
Rattus norvegicus	ENSRNOG00000033623	2 retrocopies	retro_rnor_1998, retro_rnor_2555,