RetrogeneDB ID:

retro_amel_447

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192447.1:1351614..1352057(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MSMO1
Ensembl ID:ENSAMEG00000005596
Aliases:None
Description:methylsterol monooxygenase 1 [Source:HGNC Symbol;Acc:10545]


Retrocopy-Parental alignment summary:






>retro_amel_447
ATGGCAACAAATGAAAGTATTAGCATCTTTAGTTCAGCATCCTTGGCTATGGAGTATGTAGATTCACTTTTACCTGAGAA
CCTTCTAGAAGAACAATTTAAAAATGCTTGAAACTGTATGTTGAATAATTATATAAAGTTCCAGATTGCAACTTGGGGAT
CCTTGATAGTTCATGAGGTCCTTTATTTCTTGTTCTGTTTACCTGAATTTTTGTTTCAATTTATACCTTCCATGAAAAAG
TACAAAATTCAAAAGGATAAACCAGAAACATGGAAAACCAGTGGAAATGCTTTAAAGTACTTCTCTTTAATCACTTTTGT
ATCCAGCCTCCTTTGATCTGTGGAACTTATTATTTTACAGAGTATTTTAATATACCTTATGATTGGGAAAGAATGCCAAG
ATGGTATATGCTTTTGGCAAGATGCTTTGGCTGTGCAGTGGTT

ORF - retro_amel_447 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.26 %
Parental protein coverage: 50.51 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATNESISIFSSASLAVEYVDSLLPENPLQEPFKNAWNYMLNNYTKFQIATWGSLIVHEILYFLFCLPGF
MATNESISIFSSASLA.EYVDSLLPEN.L.E.FKNA.N.MLNNY.KFQIATWGSLIVHE.LYFLFCLP.F
RetrocopyMATNESISIFSSASLAMEYVDSLLPENLLEEQFKNA*NCMLNNYIKFQIATWGSLIVHEVLYFLFCLPEF
ParentalLFQFIPYMKKYKIQKDKPETW-ENQWKCFKVILFNHFCIQPPLICGTYYFTEYFNIPYDWERMPRWCTLL
LFQFIP.MKKYKIQKDKPETW.ENQWKCFKV.LFNHFCIQPPLICGTYYFTEYFNIPYDWERMPRW..LL
RetrocopyLFQFIPSMKKYKIQKDKPETW<ENQWKCFKVLLFNHFCIQPPLICGTYYFTEYFNIPYDWERMPRWYMLL
ParentalVRCFGCAVI
.RCFGCAV.
RetrocopyARCFGCAVV

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






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_447 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_447 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 16 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000005596 1 retrocopy
retro_amel_447 ,
Choloepus hoffmanni ENSCHOG000000075502 retrocopies
retro_chof_1657, retro_chof_560,
Callithrix jacchus ENSCJAG000000093011 retrocopy
retro_cjac_2245,
Felis catus ENSFCAG000000230041 retrocopy
retro_fcat_863,
Homo sapiens ENSG000000528021 retrocopy
retro_hsap_4672,
Gorilla gorilla ENSGGOG000000157301 retrocopy
retro_ggor_2898,
Loxodonta africana ENSLAFG000000070611 retrocopy
retro_lafr_570,
Macaca mulatta ENSMMUG000000129941 retrocopy
retro_mmul_2486,
Nomascus leucogenys ENSNLEG000000065011 retrocopy
retro_nleu_2164,
Oryctolagus cuniculus ENSOCUG000000037691 retrocopy
retro_ocun_1454,
Otolemur garnettii ENSOGAG000000092812 retrocopies
retro_ogar_182, retro_ogar_3404,
Pan troglodytes ENSPTRG000000165741 retrocopy
retro_ptro_3104,
Pteropus vampyrus ENSPVAG000000137074 retrocopies
retro_pvam_1405, retro_pvam_550, retro_pvam_598, retro_pvam_784,
Sorex araneus ENSSARG000000135461 retrocopy
retro_sara_635,
Sarcophilus harrisii ENSSHAG000000001351 retrocopy
retro_shar_530,
Tursiops truncatus ENSTTRG000000128972 retrocopies
retro_ttru_20, retro_ttru_801,


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