RetrogeneDB ID:

retro_mmul_622

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:10:23126771..23127096(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ADI1
Ensembl ID:ENSMMUG00000019471
Aliases:None
Description:1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase [Source:UniProtKB/Swiss-Prot;Acc:F6QS54]


Retrocopy-Parental alignment summary:






>retro_mmul_622
ATGGTGCAGGCCTAGTACATGGATGAGCTTCCAGATGGCTGGAGGCAGCCTCACCACCCCGAGTCCCTCGCCACCCAGTG
GGCCAGAAACAGCCATGCCGGCTCAGGGCGCACTACTAAAGCTGGACACTGACAAATAAGAGAACGATCCAGAATTAGAA
AAGACTCAAAGAGAGAGAAGCTACTCCTGGATAGACATAATAAGCATATGTAAAGATAAATTACCAAATGATGAAGAAAA
CATTAAGGTGTTTTACAAGGAGCATTTACACTTGGATGATCAGATCTGTTACATCCCAGGTGGCAGTGGATACTTGGATG
ACAGA

ORF - retro_mmul_622 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.3 %
Parental protein coverage: 60.34 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMVQAWYMDDAPGDPRQPHR-PDPDRPVGLEQLRRLGVLYWKLDADKYENDPELEKIRRERNYSWMDIITI
MVQA.YMD..P...RQPH..P.P..P.G.E..........KLD.DK.ENDPELEK..RER.YSW.DII.I
RetrocopyMVQA*YMDELPDGWRQPHH>PSPSPPSGPETAMPAQGALLKLDTDK*ENDPELEKTQRERSYSWIDIISI
ParentalCKDKLPNYEEKIKMFYEEHLHLDDEIRYILDGSGYFDVR
CKDKLPN.EE.IK.FY.EHLHLDD.I.YI..GSGY.D.R
RetrocopyCKDKLPNDEENIKVFYKEHLHLDDQICYIPGGSGYLDDR

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 .00 RPM 10 .87 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 14 .44 RPM
SRP007412_cerebellum 0 .00 RPM 11 .43 RPM
SRP007412_heart 0 .00 RPM 21 .91 RPM
SRP007412_kidney 0 .00 RPM 80 .87 RPM
SRP007412_liver 0 .00 RPM 175 .95 RPM
SRP007412_testis 0 .00 RPM 9 .57 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_622 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_622 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_622 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2427
Pan troglodytes retro_ptro_1400
Gorilla gorilla retro_ggor_1510
Pongo abelii retro_pabe_1789
Parental genes homology:
Parental genes homology involve 21 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184322 retrocopies
retro_amel_1306, retro_amel_1350,
Canis familiaris ENSCAFG000000032573 retrocopies
retro_cfam_1764, retro_cfam_554, retro_cfam_603,
Choloepus hoffmanni ENSCHOG000000104968 retrocopies
retro_chof_1146, retro_chof_1212, retro_chof_1800, retro_chof_2067, retro_chof_2163, retro_chof_401, retro_chof_742, retro_chof_748,
Dasypus novemcinctus ENSDNOG000000075233 retrocopies
retro_dnov_181, retro_dnov_1891, retro_dnov_2106,
Equus caballus ENSECAG000000057651 retrocopy
retro_ecab_870,
Echinops telfairi ENSETEG000000158601 retrocopy
retro_etel_1732,
Felis catus ENSFCAG000000257632 retrocopies
retro_fcat_1465, retro_fcat_882,
Homo sapiens ENSG000001825512 retrocopies
retro_hsap_165, retro_hsap_2427,
Gorilla gorilla ENSGGOG000000348552 retrocopies
retro_ggor_1510, retro_ggor_250,
Loxodonta africana ENSLAFG000000049021 retrocopy
retro_lafr_173,
Macaca mulatta ENSMMUG00000019471 1 retrocopy
retro_mmul_622 ,
Monodelphis domestica ENSMODG000000144842 retrocopies
retro_mdom_1128, retro_mdom_723,
Nomascus leucogenys ENSNLEG000000075182 retrocopies
retro_nleu_1559, retro_nleu_237,
Oryctolagus cuniculus ENSOCUG000000005301 retrocopy
retro_ocun_1236,
Otolemur garnettii ENSOGAG000000076682 retrocopies
retro_ogar_2871, retro_ogar_535,
Pongo abelii ENSPPYG000000126832 retrocopies
retro_pabe_1789, retro_pabe_463,
Pan troglodytes ENSPTRG000000116242 retrocopies
retro_ptro_1400, retro_ptro_157,
Pteropus vampyrus ENSPVAG000000036601 retrocopy
retro_pvam_689,
Rattus norvegicus ENSRNOG000000089501 retrocopy
retro_rnor_1316,
Tarsius syrichta ENSTSYG000000041381 retrocopy
retro_tsyr_1271,
Tursiops truncatus ENSTTRG000000059422 retrocopies
retro_ttru_1485, retro_ttru_1562,


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