RetrogeneDB ID: retro_mmus_3356

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:75374608..75375811(-)
• Located in intron of: ENSMUSG00000042688

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tuba3b
• Ensembl ID: ENSMUSG00000067338
• Aliases: Tuba3b, M[a]7, Tuba7
• Description: tubulin, alpha 3B [Source:MGI Symbol;Acc:MGI:1095408]

Sequence

>retro_mmus_3356
GGAGACGACTCATTCAACACATTCTTCAGTGAGACTGCAGCTGGCACGCATGTGCCCCAGCAGTGTTTGTGGACCTGGAG
CCAACTGTGGTTGATGAAGTGCACACTGGAACCTACTGGCAGCTTTTCCACCCAAAGCAGCGGATCACTGGGAAGGAAGA
TGCTGGCAACAATTAAGCCAGAGGTCGTTATACAATTGGCAAGAAGATTGTTGACCTGGTCCTGGACAGGATCTGAAAAC
TGGCCGATCTGTGCACGGGACTTCAGGGCTTCCTCATCTTCCACAGCTTTGGAGGTAGCACAGGGTCTGTGTTTGCATCT
CTGCTGATGAAGCAGCTCTCAGCGGATTATGGCAAGAAGTCCAAGCTGGAGTTTGCCATTTACCCAGCCCCACAGGTTTC
TACAGCTGTCGTGGAGCCTTACAACTCCATCCTGACCACGCACACAACACTGGAACATTCCGACTGTGCTTTCATGGTGG
ATAATGAAGCCATCTACGACATCTGCCTGTGCAGCCTGGATATTGAACGTCCCACATACACCAACCTCAATCGTCTGATT
GGGCAGATTGTGTCATCCATCACAGCCCCCCTGAGGTTTGATGGCGCCCCGAATGTGGACTTAACAGAATTCCAGACTAA
CCTGGTGCCATATCCTCACATCCACTTCCCACTGGCAACCTATGCCCCAGTCATCTCTGCTGAGAAGGCATACCATGAGC
AGAGATCAGTGGCAGAGATCACCAATGCTTGCTTCGAGCCAGCCAATCAGATGGTCAAGTGTGACTTTCGTCACAGCAAA
TACACGGCCTGCTGCATGTTGTACAGGGGGATGTGGTTCCCAAAGATGTCAATGCACTGTTGCCACCATCAAGACCAAGC
TTGTAGATTGGTGCTGGACTGGATTTAAGGTGGGTATTAACTATCAGCCTTCTACTGTGGTCCCTGGGGGAGACCTGGCC
AAGGTGCAGCGGGCCGTGTGCATGCTGAGCAATACCACTGCCATTGCAGAGTCCTGGGCCCACCTGGACCACAAATTTGA
CCTCATGTACGCCAAGCGGGCCTTTGTGCATTGGTACGTGGGAGAAGGCATGGAGGAAGGGGAGTTCTCCGAGGCCCGGG
AGGACCTGGCAGCGCTGGAGAAGGATTATGAAGAGGTGGGCGTGGATTCCGTGGGAGCAGAGGCAGAAGAAGGGGAGGAG
TAC

Alignment

ORF - retro_mmus_3356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.73 %
• Parental protein coverage: 90.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GDDSFNTFFSETGAGKHVPR-AVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKE
          GDDSFNTFFSET.AG.HVP..AVFVDLEPTVVDEV.TGTY.QLFHP.Q.ITGKEDA.NN.ARG.YTIGK.
Retrocopy GDDSFNTFFSETAAGTHVPQ<AVFVDLEPTVVDEVHTGTYWQLFHPKQRITGKEDAGNN*ARGRYTIGKK

Parental  IVDLVLDRIRKLADLCTGLQGFLIFHSFGGGTGSGFASLLMERLSVDYGKKSKLEFAIYPAPQVSTAVVE
          IVDLVLDRI.KLADLCTGLQGFLIFHSFGG.TGS.FASLLM..LS.DYGKKSKLEFAIYPAPQVSTAVVE
Retrocopy IVDLVLDRI*KLADLCTGLQGFLIFHSFGGSTGSVFASLLMKQLSADYGKKSKLEFAIYPAPQVSTAVVE

Parental  PYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLT
          PYNSILTTHTTLEHSDCAFMVDNEAIYDIC...LDIERPTYTNLNRLIGQIVSSITA.LRFDGA.NVDLT
Retrocopy PYNSILTTHTTLEHSDCAFMVDNEAIYDICLCSLDIERPTYTNLNRLIGQIVSSITAPLRFDGAPNVDLT

Parental  EFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYR-GD
          EFQTNLVPYP.IHFPLATYAPVISAEKAYHEQ.SVAEITNACFEPANQMVKCD.RH.KY.ACCMLYR.GD
Retrocopy EFQTNLVPYPHIHFPLATYAPVISAEKAYHEQRSVAEITNACFEPANQMVKCDFRHSKYTACCMLYR<GD

Parental  VVPKDVNA-AIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARL
          VVPKDVNA...ATIKTK.....VDWC.TGFKVGINYQP.TVVPGGDLAKVQRAVCMLSNTTAIAE.WA.L
Retrocopy VVPKDVNA<TVATIKTK----LVDWCWTGFKVGINYQPSTVVPGGDLAKVQRAVCMLSNTTAIAESWAHL

Parental  DHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGVDSVEAEAEEGEEY
          DHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGVDSV.AEAEEGEEY
Retrocopy DHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGVDSVGAEAEEGEEY

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	0.07 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.15 RPM
SRP007412_liver	0.00 RPM	0.11 RPM
SRP007412_testis	0.69 RPM	924.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3356 was not detected

EST

No EST(s) were mapped for retro_mmus_3356 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_153203	1062 libraries	4 libraries	2 libraries	0 libraries	4 libraries

The graphical summary, for retro_mmus_3356 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_3356 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3356 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375, retro_fcat_647,
Monodelphis domestica	ENSMODG00000023336	1 retrocopy	retro_mdom_973,
Mustela putorius furo	ENSMPUG00000003660	1 retrocopy	retro_mputfur_130,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356 ,