RetrogeneDB ID:

retro_ptro_1666

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2B:190970640..190971164(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MED28
Ensembl ID:ENSPTRG00000015939
Aliases:None
Description:mediator complex subunit 28 [Source:HGNC Symbol;Acc:24628]


Retrocopy-Parental alignment summary:






>retro_ptro_1666
CCACCAGGTGTTATGTTCCCTGTGGAGCCACTGGGTCCCCCACCACCCCCACTGGAACTCCCAAGCTAGGCTTTGCTTCT
TCAGGAAGCTCCAGGTTCTCTAAGACCTTATGACAGTACCTTGATGGAAAAGTTGAAGTCATATTTTCAGACTTGCTTTG
CTTCTCTGGTGAGTCAGAAGTATGTCAATGGCACCAATCAGGAAGAAATTCAAACTGGTGTTGATCAGTGTATCCAGGAG
TTTCTGGATATTGCAAGACAGATAGGATGTTTTTTTCTTCAAAAAGATTGCAATTATCTGTCCAGAAACCAGATAATGCT
ATCAAAGAGGATTTCTTCGAACTAAGGAATGAATTATAGTGGAAAGACATGCTGGTCCAGAAGAACTTGACATAGTTGCG
GCATTCACGGCAGGTGCTGGAGGACATCAATGTGCAGCACAGAAAGCTAGCCGACATCCCTCAGGGTTCCTTGGCCTATC
TTGAGTAGGCATCTGCCAATATACTTGCACCTCTGAAGCCAACC

ORF - retro_ptro_1666 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.73 %
Parental protein coverage: 97.77 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPLGGMFSGQPPGPPQAPPGLPGQASLLQAAPGAPRPSSSTLVDELESSFEACFASLVSQDYVNGTDQEEI
P.G.MF...P.GPP..P..LP..A.LLQ.APG..RP..STL...L.S.F..CFASLVSQ.YVNGT.QEEI
RetrocopyPPGVMFPVEPLGPPPPPLELPS*ALLLQEAPGSLRPYDSTLMEKLKSYFQTCFASLVSQKYVNGTNQEEI
ParentalRTGVDQCIQKFLDIARQTECFFLQ-KRLQLSVQKPEQVIKEDVSELRNELQRKDALVQKHLTKLRHWQQV
.TGVDQCIQ.FLDIARQ..CFFLQ.KRLQLSVQKP...IKED..ELRNEL..KD.LVQK.LT.LRH..QV
RetrocopyQTGVDQCIQEFLDIARQIGCFFLQ<KRLQLSVQKPDNAIKEDFFELRNEL*WKDMLVQKNLT*LRHSRQV
ParentalLEDINVQHKKPADIPQGSLAYLEQASANIPAPLKPT
LEDINVQH.K.ADIPQGSLAYLE.ASANI.APLKPT
RetrocopyLEDINVQHRKLADIPQGSLAYLE*ASANILAPLKPT

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_prefrontal_cortex 0 .00 RPM 5 .99 RPM
SRP007412_cerebellum 0 .07 RPM 7 .24 RPM
SRP007412_heart 0 .06 RPM 5 .22 RPM
SRP007412_kidney 0 .10 RPM 6 .69 RPM
SRP007412_liver 0 .07 RPM 3 .83 RPM
SRP007412_testis 0 .11 RPM 4 .53 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1666 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1666 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1666 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2188
Gorilla gorilla retro_ggor_1733
Pongo abelii retro_pabe_2068
Macaca mulatta retro_mmul_916
Callithrix jacchus retro_cjac_2746

Parental genes homology:
Parental genes homology involve 22 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017601 retrocopy
Bos taurus ENSBTAG000000194411 retrocopy
Callithrix jacchus ENSCJAG000000127118 retrocopies
Cavia porcellus ENSCPOG000000126162 retrocopies
Dasypus novemcinctus ENSDNOG000000085262 retrocopies
Dipodomys ordii ENSDORG000000080421 retrocopy
Homo sapiens ENSG000001185795 retrocopies
Gorilla gorilla ENSGGOG000000011145 retrocopies
Loxodonta africana ENSLAFG000000169361 retrocopy
Microcebus murinus ENSMICG000000067922 retrocopies
Myotis lucifugus ENSMLUG000000013511 retrocopy
Macaca mulatta ENSMMUG000000057345 retrocopies
Monodelphis domestica ENSMODG000000008131 retrocopy
Nomascus leucogenys ENSNLEG000000166203 retrocopies
Oryctolagus cuniculus ENSOCUG000000015764 retrocopies
Otolemur garnettii ENSOGAG000000338354 retrocopies
Ochotona princeps ENSOPRG000000039322 retrocopies
Pongo abelii ENSPPYG000000146274 retrocopies
Pan troglodytes ENSPTRG00000015939 3 retrocopies
retro_ptro_1424, retro_ptro_1666 , retro_ptro_431,
Pteropus vampyrus ENSPVAG000000157161 retrocopy
Ictidomys tridecemlineatus ENSSTOG0000000093010 retrocopies
Tursiops truncatus ENSTTRG000000061771 retrocopy



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