RetrogeneDB ID: retro_mmus_1489

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:13779819..13780163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tceb2
• Ensembl ID: ENSMUSG00000055839
• Aliases: Tceb2, 0610040H15Rik
• Description: transcription elongation factor B (SIII), polypeptide 2 [Source:MGI Symbol;Acc:MGI:1914923]

Sequence

>retro_mmus_1489
ATGGCTGTGTTTCTCATGACCCCACACAAGAAGACCACCATCTTCACTGAGGCCAAGGAGTCAAGCTTGGTGTTGGCACT
CAAGCGCATCATTGAGGGCATCATGAAGAGGCCTCCTGAGGAGAGCTGCTGTTCAAGGACAACCAGCTCCTTGATGAGAA
AACTCTGGGGGAATGTGGCTTCACTAGTCAGGTAGCAAAGCCACAGGCCCCAGCCACAGTGGGCCTGGCCTTCAGAGCAG
AAGATGCCTTTGAAGGCCTGCCTATCTACCCCAATTCTTGTCCTCCAGAACTTCCAGGTGTGATGAAGGATTCTGGAAAT
AGTGCTAAGGAACAAGTTGTACAG

Alignment

ORF - retro_mmus_1489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPEE-QRLYKDDQLLDDGKTLGECGFTSQTARP
          M.VFLM....KTTIFT.AKESS.V..LKRI.EGI.KRPPEE...L.KD.QLLD..KTLGECGFTSQ.A.P
Retrocopy MAVFLMTPHKKTTIFTEAKESSLVLALKRIIEGIMKRPPEE<ELLFKDNQLLDE-KTLGECGFTSQVAKP

Parental  QAPATVGLAFRADDTFEALRIEPFSSPPELPDVMKPQDSGGSANEQAVQ
          QAPATVGLAFRA.D.FE.L.I.P.S.PPELP.VMK..DSG.SA.EQ.VQ
Retrocopy QAPATVGLAFRAEDAFEGLPIYPNSCPPELPGVMK--DSGNSAKEQVVQ

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	0.19 RPM	34.18 RPM
SRP007412_cerebellum	0.04 RPM	20.36 RPM
SRP007412_heart	0.12 RPM	27.80 RPM
SRP007412_kidney	0.19 RPM	19.50 RPM
SRP007412_liver	0.05 RPM	14.88 RPM
SRP007412_testis	0.14 RPM	71.72 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1489 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	16:13780449..13781011
ENCFF001YIJ	POLR2A	16:13779945..13781469
ENCFF001YKA	POLR2A	16:13779151..13782127

EST

No EST(s) were mapped for retro_mmus_1489 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_44943	156 libraries	265 libraries	638 libraries	12 libraries	1 library

The graphical summary, for retro_mmus_1489 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_1489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1489 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019543	3 retrocopies	retro_btau_142, retro_btau_17, retro_btau_29,
Callithrix jacchus	ENSCJAG00000015347	10 retrocopies	retro_cjac_1593, retro_cjac_1606, retro_cjac_2051, retro_cjac_2613, retro_cjac_2987, retro_cjac_3030, retro_cjac_342, retro_cjac_3819, retro_cjac_639, retro_cjac_959,
Cavia porcellus	ENSCPOG00000021024	1 retrocopy	retro_cpor_1416,
Felis catus	ENSFCAG00000004711	2 retrocopies	retro_fcat_112, retro_fcat_40,
Homo sapiens	ENSG00000103363	2 retrocopies	retro_hsap_1246, retro_hsap_940,
Gorilla gorilla	ENSGGOG00000015306	1 retrocopy	retro_ggor_976,
Monodelphis domestica	ENSMODG00000016536	4 retrocopies	retro_mdom_1149, retro_mdom_1617, retro_mdom_1964, retro_mdom_23,
Mustela putorius furo	ENSMPUG00000015265	1 retrocopy	retro_mputfur_469,
Mus musculus	ENSMUSG00000055839	7 retrocopies	retro_mmus_1212, retro_mmus_1489 , retro_mmus_1664, retro_mmus_2930, retro_mmus_511, retro_mmus_747, retro_mmus_99,
Nomascus leucogenys	ENSNLEG00000009471	2 retrocopies	retro_nleu_295, retro_nleu_89,
Oryctolagus cuniculus	ENSOCUG00000010116	2 retrocopies	retro_ocun_202, retro_ocun_930,
Pongo abelii	ENSPPYG00000007013	1 retrocopy	retro_pabe_74,
Pan troglodytes	ENSPTRG00000007663	1 retrocopy	retro_ptro_857,
Rattus norvegicus	ENSRNOG00000004814	6 retrocopies	retro_rnor_1226, retro_rnor_1275, retro_rnor_185, retro_rnor_1948, retro_rnor_35, retro_rnor_352,
Sus scrofa	ENSSSCG00000008061	1 retrocopy	retro_sscr_858,