RetrogeneDB ID: retro_mmus_158

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:7179364..7180699(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000095159
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_158
ATGAGGGAGATCGTGCACCTGCAGGCTGGGCAGTGCGGCAACCAGATTGGCGCCAAGTTCTGGGAGGTAATCAGTGACGA
GCATGGCATTGATACCACTGGCACTTACCACGGAGATAGCGACCTCCAGCTGGAGCGCATCAATGTGTATTACAACGAAG
CCACCGGTGGCAAGTATGTGCCCCGCGCCGTGCTCGTGGACTTGGAGCCCTGCACCATGGACTCGGTTCGTTCAGGGCCC
TTCGGGCAGATCTTCAGACCTGATAACTTCGTCTTTGGTCAGAGTGGGGCTGGGAACAACTGGGCCAAGGGGCACTACAC
AGAAGGTGCAGAGCTGGTTGACTCGGTGTTGGACGTTGTGAGAAAGGAAGCTGAGAGCTGTGACTGCCTGCAGGGCTTCC
AGCTGACCCACTCCCTGGGTGGGGGGACTGGGTCTGGGATGGGTACCCTCATCAGCAAGATCCGGGAGGAGTACCCAGAC
AGAATCATGAACACCTTCAGTGTGGTACCTTCCCCCAAGGTGTCGGACACAGTGGTTGAGCCCTACAATGCCACCCTTTC
AGTCCATCAGCTGGTTGAAAACACAGATGAGACCTATTGTATTGATGATGAAGCACTCTATGACATCTGCTTCAGAACCC
TAAAGCTGACCACACCCACTTACGGTGACCTGAACCATCTAGTGTCCGCCACCATGAGTGGGGTAACCACTTGCCTGCGA
TTCCCTGGCCAGCTAAATGCTGACCTGCGGAAACTGGCTGTAAATATGGTGCCCTTCCCTCGCCTGCACTTCTTCATGCC
TGGCTTTGCCCCCTTGACCAGCCGGGGAAGCCAGCAGTACCGTGCCCTGACAGTTCCTGAGCTCACCCAGCAGATGTTTG
ATGCCAAGAACATGATGGCTGCCTGTGATCCAAGACATGGGCGCTACTTGACTGTGGCTGCCGTGTTCAGGGGCCGCATG
TCTATGAAGGAGGTGGACGAACAGATGCTTAATGTCCAAAACAAGAACAGCAGCTACTTTGTTGAGTGGATCCCCAACAA
TGTGAAGACAGCTGTCTGTGACATTCCACCTCGGGGCCTGAAAATGTCCACCACCTTCATTGGCAACAGCACCGCTATCC
AGGAGCTGTTCAAACGCATCTCAGAGCAGTTCACAGCCATGTTCCCACGCAAGACCTTCCTACATTGGTACACGGGTGAG
GGCATGGATGAGATGGAGTTCACTGAGGCTGAGAGCAACATGAACGACCTGGTGTCCGAGTACCAGCAGTACCAGGATGC
TACAGCTGAGGAAGAGGGAGAGTATGAGGAGGAGGCTGAGGAGGAGGTGGCTTAG

Alignment

ORF - retro_mmus_158 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
          MREIVHLQAGQCGNQIGAKFWEVISDEHGID.TGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
Retrocopy MREIVHLQAGQCGNQIGAKFWEVISDEHGIDTTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          .TMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
Retrocopy CTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          GGTGSGMGTL.ISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCID.EALYDI
Retrocopy GGTGSGMGTL-ISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDDEALYDI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
          CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
Retrocopy CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ

Parental  YRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
          YRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
Retrocopy YRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK

Parental  TAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
          TAVCDIPPRGLKMS.TFIGNSTAIQELFKRISEQFTAMF.RK.FLHWYTGEGMDEMEFTEAESNMNDLVS
Retrocopy TAVCDIPPRGLKMSTTFIGNSTAIQELFKRISEQFTAMFPRKTFLHWYTGEGMDEMEFTEAESNMNDLVS

Parental  EYQQYQDATAEEEGEFEEEAEEEVA
          EYQQYQDATAEEEGE.EEEAEEEVA
Retrocopy EYQQYQDATAEEEGEYEEEAEEEVA

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	0.84 RPM	107.19 RPM
SRP007412_cerebellum	1.56 RPM	92.70 RPM
SRP007412_heart	0.16 RPM	76.24 RPM
SRP007412_kidney	1.44 RPM	65.66 RPM
SRP007412_liver	0.41 RPM	31.05 RPM
SRP007412_testis	33.16 RPM	443.58 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_158 was not detected

EST

No EST(s) were mapped for retro_mmus_158 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_115115	196 libraries	306 libraries	237 libraries	179 libraries	154 libraries

The graphical summary, for retro_mmus_158 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_158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_158 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,