RetrogeneDB ID:

retro_mmus_2947

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:80507795..80508251(+)
Located in intron of:ENSMUSG00000030528
Retrocopy
information
Ensembl ID:ENSMUSG00000091989
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ndufab1
Ensembl ID:ENSMUSG00000030869
Aliases:None
Description:NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1 [Source:MGI Symbol;Acc:MGI:1917566]


Retrocopy-Parental alignment summary:






>retro_mmus_2947
GTCCTCTGCGCCTGTGTCCGCCGCCTGCCCGCGGCCTTCGCGCCGCTGCCCCGGCTTCCCACGTTGGCCTTGGCGTGGCC
GCTCAGCACCACCCTATGCCCTGAGGGAATCCGGAGGAGACCCGGGGCTCTGCAGTCCGCCTTGGCGCTCGCGCAGGTGC
CTGGAACAGTCACACATTTGTGCCGCCAGTACAGTGACGCACCCCCACTGACGTTAGACGGAATCAAGGACCGAGTTCTG
TATGTCTTGAAACTCTATGATAAGATTGATCCAGAAAAGCTCTCCGTAAATTCTTATTTTATGAAGGACCTGGGCTTAGA
CAGTTTGGACCAAGTGGAAATTATTATGGCCATGGAAGACGAATTTGGGTTTGAAATTCCTGATATAGATGCAGAGAAGT
TAATGTGTCCACAAGAAATTGTAGATTACATTGCAGATAAGAAGGATGTGTATGAA

ORF - retro_mmus_2947 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.68 %
Parental protein coverage: 97.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPL
VLCACVRRLPAAFAPLPRLPTLALA.PLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPL
RetrocopyVLCACVRRLPAAFAPLPRLPTLALAWPLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPL
ParentalTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEI
TLDGIKDRVLYVLKLYDKIDPEKLSVNS.FMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEI
RetrocopyTLDGIKDRVLYVLKLYDKIDPEKLSVNSYFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEI
ParentalVDYIADKKDVYE
VDYIADKKDVYE
RetrocopyVDYIADKKDVYE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .02 RPM 20 .21 RPM
SRP007412_cerebellum 0 .04 RPM 27 .01 RPM
SRP007412_heart 0 .06 RPM 57 .56 RPM
SRP007412_kidney 0 .00 RPM 47 .18 RPM
SRP007412_liver 0 .03 RPM 19 .63 RPM
SRP007412_testis 0 .00 RPM 6 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2947 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2947 retrocopy.

TSS - click to see more details



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_137494141 libraries409 libraries490 libraries23 libraries9 libraries

The graphical summary, for retro_mmus_2947 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_2947 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2947 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000143041 retrocopy
retro_amel_1692,
Canis familiaris ENSCAFG000000176673 retrocopies
retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni ENSCHOG000000035582 retrocopies
retro_chof_1517, retro_chof_2498,
Callithrix jacchus ENSCJAG000000206162 retrocopies
retro_cjac_2635, retro_cjac_3099,
Cavia porcellus ENSCPOG000000120382 retrocopies
retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus ENSDNOG000000171225 retrocopies
retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus ENSFCAG000000132413 retrocopies
retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Homo sapiens ENSG000000047791 retrocopy
retro_hsap_3484,
Gorilla gorilla ENSGGOG000000063201 retrocopy
retro_ggor_2349,
Loxodonta africana ENSLAFG000000010321 retrocopy
retro_lafr_330,
Macropus eugenii ENSMEUG000000126813 retrocopies
retro_meug_1780, retro_meug_303, retro_meug_830,
Microcebus murinus ENSMICG000000077782 retrocopies
retro_mmur_1193, retro_mmur_120,
Macaca mulatta ENSMMUG000000205221 retrocopy
retro_mmul_101,
Monodelphis domestica ENSMODG000000163521 retrocopy
retro_mdom_389,
Mustela putorius furoENSMPUG000000121422 retrocopies
retro_mputfur_1135, retro_mputfur_466,
Mus musculus ENSMUSG00000030869 6 retrocopies
retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947 , retro_mmus_3094, retro_mmus_3332,
Oryctolagus cuniculus ENSOCUG000000084571 retrocopy
retro_ocun_1712,
Otolemur garnettii ENSOGAG000000055622 retrocopies
retro_ogar_2916, retro_ogar_325,
Pongo abelii ENSPPYG000000071921 retrocopy
retro_pabe_2879,
Pan troglodytes ENSPTRG000000078891 retrocopy
retro_ptro_2358,
Rattus norvegicus ENSRNOG000000181292 retrocopies
retro_rnor_1353, retro_rnor_2058,
Sus scrofa ENSSSCG000000107951 retrocopy
retro_sscr_1017,
Ictidomys tridecemlineatus ENSSTOG000000246572 retrocopies
retro_itri_281, retro_itri_916,
Tursiops truncatus ENSTTRG000000052582 retrocopies
retro_ttru_1229, retro_ttru_989,


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