RetrogeneDB ID:

retro_mmul_2335

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:8:40558451..40559054(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000019307
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NFYB
Ensembl ID:ENSMMUG00000022570
Aliases:None
Description:nuclear transcription factor Y subunit beta [Source:RefSeq peptide;Acc:NP_001244649]


Retrocopy-Parental alignment summary:






>retro_mmul_2335
CTGGAGATGAATGGGGACCGCTGTATGACATGTGCTTCTGCACCGGGAATTTCCGAAGACTGCACTGGAGGAGTCATTAT
GTTATACAGCCTCATGATGACAGTGAGGACAGCATGAATGGTCAAGAAGATACAAATGGTTCAAAAGAAAGTTGCAGAGA
ACAAAATATACATTTTTTGATTGCACATGTCACTGGGATAATGAAACATGCCATATCTCAAATGGGAAATGCCCAAGAAA
GTGTTCAAGAATGTGTACGTGCGTTCATCAGCTTTATAACACCTGAGGTAACTGAAAGACGCCCCCAAGAGAAACGGAAA
TGACCAGTGGAGAGGATCTTCTCTTTGCCGTGTCTGCCGTAGGCTTCGACAGTTATGTGGAACCTCTGAAATTATCCCTT
CAGAAACTCAGAGAGGCTATGAAAAGAGAGAAGGGAATTGGTAGAGAAGTCAGAGCTACAGATGGGCTAAGTGAGGAGCT
TACAGAATAGGCATTTGCTAGCCAGTCACCAGCCGGCTTCATACCTGCCGCTGGGCAACAACAAATGTTATGGTTTATAT
ACCACCATAGCAAGAGATTTCTGGTGTTCGACAAAGTCTGTTT

ORF - retro_mmul_2335 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.55 %
Parental protein coverage: 99.52 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMTMDGDSSTTDASQLGISADYIGG-SHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMK
..M.GD...T.AS..GIS.D..GG.SHYVIQPHDD.EDSMN..EDTNGSKES.REQ.I...IA.V..IMK
RetrocopyLEMNGDRCMTCASAPGISEDCTGG<SHYVIQPHDDSEDSMNGQEDTNGSKESCREQNIHFLIAHVTGIMK
ParentalNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK-TINGEDILFAMSTLGFDSYVEPLKLYL
.AI.Q.G.....A.E.VQECV..FISFIT.E..ER..QEKRK....GED.LFA.S..GFDSYVEPLKL.L
RetrocopyHAISQMG----NAQESVQECVRAFISFITPEVTERRPQEKRK<MTSGEDLLFAVSAVGFDSYVEPLKLSL
ParentalQKFREAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLITTDGQQQ-NVMVYTTSYQQISGVQQIQF
QK.REAMK.EKGIG..V.ATDGLSEELTE.AF..Q.PAG.I...GQQQ.NVMVY....Q.ISGV.Q..F
RetrocopyQKLREAMKREKGIGREVRATDGLSEELTE*AFASQSPAGFIPAAGQQQ<NVMVYIPP*QEISGVRQSLF

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






(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 .00 RPM 22 .52 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 11 .66 RPM
SRP007412_cerebellum 0 .00 RPM 14 .92 RPM
SRP007412_heart 0 .00 RPM 6 .71 RPM
SRP007412_kidney 0 .35 RPM 12 .68 RPM
SRP007412_liver 1 .78 RPM 7 .36 RPM
SRP007412_testis 0 .00 RPM 7 .95 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_2335 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_2335 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2335 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066861 retrocopy
Bos taurus ENSBTAG000000307441 retrocopy
Canis familiaris ENSCAFG000000291771 retrocopy
Callithrix jacchus ENSCJAG000000146101 retrocopy
Cavia porcellus ENSCPOG000000032131 retrocopy
Felis catus ENSFCAG000000264711 retrocopy
Homo sapiens ENSG000001208372 retrocopies
Gorilla gorilla ENSGGOG000000088661 retrocopy
Myotis lucifugus ENSMLUG000000054681 retrocopy
Macaca mulatta ENSMMUG00000022570 3 retrocopies
retro_mmul_1433, retro_mmul_2119, retro_mmul_2335 ,
Mustela putorius furoENSMPUG000000120643 retrocopies
Nomascus leucogenys ENSNLEG000000065432 retrocopies
Oryctolagus cuniculus ENSOCUG000000044154 retrocopies
Ochotona princeps ENSOPRG000000081172 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000052791 retrocopy
Tupaia belangeri ENSTBEG000000057311 retrocopy



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