RetrogeneDB ID: retro_mmus_3139

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:62539840..62540468(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tra2b
• Ensembl ID: ENSMUSG00000022858
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:106016]

Sequence

>retro_mmus_3139
TCCCAGAGCAGGTCTTACAGCCGAGATTATCGCAGGTGCCACAGCCACATCATTCTCCCATGTCTACTGTCAAGTCTCAT
GTTGGAAACTGGGCAAATCCAGACCCCAACTGTTGTCTTGGAGTATTTGGGTTAAGCTTATACACCACAGAAAGTTATCT
AAGAGAAGTGTTCTCTAAATATAACCCTATTTGCTGATGTGTCTTTTGTATATGACCAGCAGTCTAGACGCTCAAGAGGA
TTTGCCTTTGTATATTTTGAAAATGCAGATGATACCAATGAGGCTAAAGAACGTGCCAATGGATTGGAGCTTGATGAGAG
ACGAATTAGGGTCGATTTCTCTATAACAAAAGACCTCGTACACCAACACCAGGAATTTATATGGGGAGACCCACTTATGA
CAGTTCACGCCACCGAGACTATTATGACAGAGGACATGATAGGAGATATGCTGGCCGGGACTGTTACAGCAGATCATACA
GCGGAGGAGGAGGTAGAAGAGGAGGTGGATGGAGAGCAACTCAAGACGGATCAGATTTACACAAGATGGTCACCTTCTCC
ATACATACTACAGTGGTGGAGGATACGGGTCATGTTCTCGATCGTGATCCTACTCACTTCGTCACTAT

Alignment

ORF - retro_mmus_3139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.7 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SRSRSYSRDYRRRHSH-SHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPI-ADVS
          S.SRSYSRDYRR.HSH..HSPMST...HVGN.ANPDPNCCLGVFGLSLYTTE..LREVFSKY.PI.ADVS
Retrocopy SQSRSYSRDYRRCHSH<HHSPMSTVKSHVGNWANPDPNCCLGVFGLSLYTTESYLREVFSKYNPI>ADVS

Parental  IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT-KRPHTPTPGIYMGRPTYGSSR
          .VYDQQSRRSRGFAFVYFEN.DD..EAKERANG.ELD.RRIRVDFSIT.KRP.TPTPGIYMGRPTY.SSR
Retrocopy FVYDQQSRRSRGFAFVYFENADDTNEAKERANGLELDERRIRVDFSIT<KRPRTPTPGIYMGRPTYDSSR

Parental  RRDYYDRGYDRGYDDRDYYSRSYRGGGG-GGGGWRAAQDRDQIYRRRSPSPY-YSRGG-YRSRSRSRSYS
          .RDYYDRG.DR.Y..RD.YSRSY.GGGG..GGGWRA.QD..........S...Y..GG.Y.S.SRS.SYS
Retrocopy HRDYYDRGHDRRYAGRDCYSRSYSGGGGRRGGGWRATQDGSDLHKMVTFSIH<YYSGGGYGSCSRS*SYS

Parental  PRRY
          .R.Y
Retrocopy LRHY

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	36.47 RPM
SRP007412_cerebellum	0.00 RPM	41.08 RPM
SRP007412_heart	0.00 RPM	31.25 RPM
SRP007412_kidney	0.00 RPM	45.26 RPM
SRP007412_liver	0.00 RPM	29.14 RPM
SRP007412_testis	0.00 RPM	82.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3139 was not detected

EST

No EST(s) were mapped for retro_mmus_3139 retrocopy.

TSS

No TSS is located nearby retro_mmus_3139 retrocopy 5' end.

Lab

retro_mmus_3139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001697	2 retrocopies	retro_btau_1245, retro_btau_850,
Myotis lucifugus	ENSMLUG00000005781	2 retrocopies	retro_mluc_2565, retro_mluc_2567,
Mustela putorius furo	ENSMPUG00000003157	1 retrocopy	retro_mputfur_673,
Mus musculus	ENSMUSG00000022858	6 retrocopies	retro_mmus_1187, retro_mmus_2253, retro_mmus_2313, retro_mmus_3139 , retro_mmus_3617, retro_mmus_756,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Ochotona princeps	ENSOPRG00000007990	2 retrocopies	retro_opri_24, retro_opri_930,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,