RetrogeneDB ID: retro_mmus_3297

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:91097147..91098497(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000056904
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tuba1b
• Ensembl ID: ENSMUSG00000023004
• Aliases: Tuba1b, Tuba2
• Description: tubulin, alpha 1B [Source:MGI Symbol;Acc:MGI:107804]

Sequence

>retro_mmus_3297
ATGCGTGAGTGCATCTCCATCCACGTTGGCCAGGCTGGTGTCCAGATCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCATCCAGGCTGATGGCCAGATGCCAAGTGGCAAGACCATTCGGGGAGGAGATGACTCCTTCAACACCTTCAGTG
AGACAGGAGCTGGCAAGCATGTGCCCCGGGCAGTGTTCGTAGACCTGGAACCCACAGTCATCGATGAAGTTCGCACTGGC
ACCTACCGCCAGCTCTTCCACCCTGAGCAACTCATCACAGGCAAGGAGGATGCTGCCAATAACTATGCCCGTGGCCACTA
CACCATTGGCAAGGAGATCATTGACCTTGTCCTGGACACGATTCGCAAGCTGGCTGACCAGTGCATAGGTCTCCAGGGCT
TCTTGGTTTTCCACAGCTTTGGCGGGGGAACTGGCTCTGGCTTCACCTCCCTGCTGATGGAGCGGCTCTCTGTGGATTAC
GGAAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTTTCCACTGCTGTGGTTGAGCCCTACAATTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCGTA
GAAACCTCGACATTGAGCACCCAACCTACACCAACCTTAACCGCCTTATTAGCCAGATTGTGTCTTCCATCACTGCTTCC
CTCAGATTTGATGGGGCCCTGAATGTTGATCTGACAGAATTCCAGACCAACCTGGTACCCTACCCTCGCATCCACTTCCC
TCTGGCCACTTATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAGCACCTTTCTGTAGCAGAGATCACCAATGCCT
GCTTTGAGCCAGCCAACCAGATGGTAAAATGTGACCCTCGCCATGGTAAATACATGGCTTGCTGCCTGCTGTACCGTGGT
GATGTGATTCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAGACCAAGCGCAGTATCCAGTTTGTAGACTGGTGTCC
CACTGGCTTCAAGGTTGGCATTAATTACCAGCCTCCCACTGTGGTACCCGGTGGTGACCTGGCCAAGGTGCAGAGAGCTG
TGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCATGGGCTCGCCTAGATCACAAGTTTGATCTGATGTATGCCAAG
CGTGCCTTTGTGTACTGGTATGTGGGTGAGAGCATGGAGGAGGGTGAGTTCTCTGAGGCCCGTGAGGACATGGCTGCCCT
AGAGAAGGATTATGAGGAGGTTGGTGTGGATTCTGTGGAAGGCGAGGGGGAGGAAGAAGGAGAGGAATAC

Alignment

ORF - retro_mmus_3297 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIHVGQAGVQIGNACWELYCLEHGIQ.DGQMPS.KTI.GGDDSFNTF.SETGAGKHVPRAVFVDL
Retrocopy MRECISIHVGQAGVQIGNACWELYCLEHGIQADGQMPSGKTIRGGDDSFNTF-SETGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD.IRKLADQC.GLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDTIRKLADQCIGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DICRRNLDIE.PTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
Retrocopy DICRRNLDIEHPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
          AYHE.LSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDV.PKDVNAAIATIKTKRSIQFVDWCPTG
Retrocopy AYHEHLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVIPKDVNAAIATIKTKRSIQFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFV.WYVGE.MEEGEFSE
Retrocopy FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVYWYVGESMEEGEFSE

Parental  AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
Retrocopy AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

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	0.56 RPM	77.45 RPM
SRP007412_cerebellum	0.91 RPM	63.92 RPM
SRP007412_heart	1.53 RPM	36.14 RPM
SRP007412_kidney	0.29 RPM	16.90 RPM
SRP007412_liver	0.11 RPM	8.82 RPM
SRP007412_testis	0.59 RPM	8.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3297 was not detected

EST

No EST(s) were mapped for retro_mmus_3297 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_153938	662 libraries	292 libraries	118 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_3297 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_3297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3297 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
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,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,