RetrogeneDB ID: retro_mmus_422

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:24594429..24595423(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tubb4b
• Ensembl ID: ENSMUSG00000036752
• Aliases: Tubb4b, 4930542G03Rik, Tubb2c, Tubb2c1
• Description: tubulin, beta 4B class IVB [Source:MGI Symbol;Acc:MGI:1915472]

Sequence

>retro_mmus_422
ATGAGGGAGATCATGCACCTGCAGGCTGGGCACTGCGGCAACCAGATTGGCGCCAAGTTCTGGGAGGTAATCAGCGACAA
GCATGGCATTGATCCCACTGGCACTTACCACGGAGATAGCGACCTCCAGCTGGAGCGCATCAACGTGTACTACAACGAAG
CCACCAGTGGAAAGTATGTGCCCCGTGCCGTGCTTCTGGACTTGGAGCCGGGAACCATGGACTCTGTGCGTTCAGGGCCC
TTCGGGCAGATCTTCAGACCTGATAACTTCTTCTTTGGTCAGAGTGGGGCTGGGAACAACTGGGCCAAGAGGCACTACAC
AGAAGGTGCAGAGCTGGTTGACTCGATGTTGGACATTGTGAGAAAGGAAGCTGAGAGCTGTGACTGCCTACAGGGCTTCC
AGCTGAACCACTCCATGGGTGGGGGGACTGGGTCTGGGATGGGTACCCTCCTTATCAGCAAGATCTGGGAGGAGTACCCA
GACAGAATCATGAACACCTTCAGTGTGGTACCTTCCCCCAAGGTGTCGGACACAGTGGTTGAGCCCTACAATGCCAGCCT
TTCAGTCCACCAGCTGGTTGAAAACACAGATGAGACCTCTTGTATTGATAATGAAGCACTCTAGGACATCTGCTTCAAAA
CCTTAAAGCTGACCACACCCACTTATGGTTACCTGAATCATCTAGTGTCTGCCACCATGAGTGGGGTAACCACTTGCCTG
CGATTCCCTGGCCAGCTAAATGCTGACCTGCGGAAACTGGCTGGTAAATATGGTGCCCTTCCCTCGCCTGCACTTCTTCA
TGCCTGGCTTTGCCCCCTTGACCAGCCGGGGAAGCCAGCAGTACCGTGCCCTGACAGTTCCTGAGCTCACCCAGCAGATG
TTTGATGCCAAGAACATGATGGCTGCCTGTGATCCAAGACATGGGCGCTACTTGACTGTGGCTGCCGTGTTCAGGGGCCG
CATGTCTATGGAGGAGGTGGACGAACAGATGCTT

Alignment

ORF - retro_mmus_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.28 %
• Parental protein coverage: 74.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
          MREI.HLQAG.CGNQIGAKFWEVISD.HGIDPTGTYHGDSDLQLERINVYYNEAT.GKYVPRAVL.DLEP
Retrocopy MREIMHLQAGHCGNQIGAKFWEVISDKHGIDPTGTYHGDSDLQLERINVYYNEATSGKYVPRAVLLDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDSVRSGPFGQIFRPDNF.FGQSGAGNNWAK.HYTEGAELVDS.LD.VRKEAESCDCLQGFQL.HS.G
Retrocopy GTMDSVRSGPFGQIFRPDNFFFGQSGAGNNWAKRHYTEGAELVDSMLDIVRKEAESCDCLQGFQLNHSMG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          GGTGSGMGTLLISKI.EEYPDRIMNTFSVVPSPKVSDTVVEPYNA.LSVHQLVENTDET.CIDNEAL.DI
Retrocopy GGTGSGMGTLLISKIWEEYPDRIMNTFSVVPSPKVSDTVVEPYNASLSVHQLVENTDETSCIDNEAL*DI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLA-VNMVPFPRLHFFMPGFAPLTSRGSQ
          CF.TLKLTTPTYG.LNHLVSATMSGVTTCLRFPGQLNADLRKLA.VNMVPFPRLHFFMPGFAPLTSRGSQ
Retrocopy CFKTLKLTTPTYGYLNHLVSATMSGVTTCLRFPGQLNADLRKLA>VNMVPFPRLHFFMPGFAPLTSRGSQ

Parental  QYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQML
          QYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSM.EVDEQML
Retrocopy QYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMEEVDEQML

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	0.28 RPM	107.19 RPM
SRP007412_cerebellum	0.26 RPM	92.70 RPM
SRP007412_heart	0.09 RPM	76.24 RPM
SRP007412_kidney	0.40 RPM	65.66 RPM
SRP007412_liver	0.19 RPM	31.05 RPM
SRP007412_testis	6.04 RPM	443.58 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_422 was not detected

EST

No EST(s) were mapped for retro_mmus_422 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_73711	431 libraries	503 libraries	135 libraries	3 libraries	0 libraries

The graphical summary, for retro_mmus_422 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_422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_422 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016380	2 retrocopies	retro_amel_817, retro_amel_868,
Cavia porcellus	ENSCPOG00000011966	1 retrocopy	retro_cpor_497,
Microcebus murinus	ENSMICG00000010939	1 retrocopy	retro_mmur_792,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849, retro_mmul_2533,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117,
Mus musculus	ENSMUSG00000016255	1 retrocopy	retro_mmus_1109,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422 ,
Otolemur garnettii	ENSOGAG00000005927	2 retrocopies	retro_ogar_3410, retro_ogar_3450,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867,