RetrogeneDB ID: retro_mmus_1660

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:70393037..70393466(-)
• Located in intron of: ENSMUSG00000003279

Retrocopy information

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

Parental gene information

• Parental gene symbol: Stmn1
• Ensembl ID: ENSMUSG00000028832
• Aliases: Stmn1, 19k, Lag, Lap18, Op18, P18, P19, Pig, Pp17, Pp18, Pp19, Pr22, Smn
• Description: stathmin 1 [Source:MGI Symbol;Acc:MGI:96739]

Sequence

>retro_mmus_1660
ATGGCATCTTCTGATATTCAGGTGAAAGAGCTGGAGAAGTGTGCTTCAGGCCAGGCTTTTGAGCTGATTCTCAGCCCTCG
GTCAAAAGAATCTGTCCCCGATTTTCCCCCCTCCCCCCAAAGAAGAAGGACCTTTCCCTGGAGGAAAATCCAGAAGAAAT
TAGAAGCTGCAGAAAAAAGACGCAAGTCTCATGAAGCGGAAGTCTTGAGGCAGCTTGCCGAGAAGCGGGAGCATGCAAGA
GACGTGCTCCAGAAAGCCATCGAGGAGAACAACAACTTCAGCAAAGTGGCGGAGGAGAAACTGACCCACAAAATGGAGAC
TAACAAAGAGAACCGAGAGGCGTAAATGGCGGCCAAGCTGGAGCGCTTGCCAGAGAAGGACACACGTTGCAAAGGTGCGG
AAGAACAAAGAATCCAAAGACCCCGCGGA

Alignment

ORF - retro_mmus_1660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASSDIQVKELEKRASGQAFELILSPRSKESVPDF-PLSPPKKKDLSLEE-IQKKLEAAEERRKSHEAEV
          MASSDIQVKELEK.ASGQAFELILSPRSKESVPDF......KKKDLSLEE.IQKKLEAAE.RRKSHEAEV
Retrocopy MASSDIQVKELEKCASGQAFELILSPRSKESVPDF<XXXXXKKKDLSLEE>IQKKLEAAEKRRKSHEAEV

Parental  LKQLAEKREHEKEVLQKAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKFLPGQARGRGAE
          L.QLAEKREH...VLQKAIEENNNFSK.AEEKLTHKME.NKENREA.MAAKLERL.EK......R..GAE
Retrocopy LRQLAEKREHARDVLQKAIEENNNFSKVAEEKLTHKMETNKENREA*MAAKLERLPEK----DTRCKGAE

Parental  EQRIQRPRG
          EQRIQRPRG
Retrocopy EQRIQRPRG

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	81.47 RPM
SRP007412_cerebellum	0.09 RPM	59.88 RPM
SRP007412_heart	0.00 RPM	2.40 RPM
SRP007412_kidney	0.00 RPM	6.99 RPM
SRP007412_liver	0.03 RPM	1.34 RPM
SRP007412_testis	0.00 RPM	54.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1660 was not detected

EST

No EST(s) were mapped for retro_mmus_1660 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_56299	415 libraries	413 libraries	227 libraries	12 libraries	5 libraries

The graphical summary, for retro_mmus_1660 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_1660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660 , retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806, retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,