RetrogeneDB ID:

retro_tsyr_1453

Retrocopy
location
Organism:Tarsier (Tarsius syrichta)
Coordinates:scaffold_446477:496..892(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHMP4B
Ensembl ID:ENSTSYG00000013212
Aliases:None
Description:charged multivesicular body protein 4B [Source:HGNC Symbol;Acc:16171]


Retrocopy-Parental alignment summary:






>retro_tsyr_1453
TCAACCCCGGCGTTCGAGCGAGAGGCCTGAGCATGCCAGCCTGGCGCCCAGGCACTCAGGGGCGTGGGCTGTGCTGCCGT
GGCCACGAAGGCCACTGGGGGAGCGCAGACATCGACAAAGCTGATGTGCTCCTGCGGGCCGCTGCCCACCCACAGGAACT
TGCTGAGGTGGTTTCCAGACCTTCGGGTTTGGAGAAGACTTCGAGGAGGATGAGCTCATGGCAGGATTAGAAGACCTAGA
ACAGGTGAACTTGACAAGGACTAGATGGAAACCAGTGGGCCTGAGCCAGTTCTTCCACCAAATGTCCTCTCCATCGGCCT
CCCATCAAAACACGCCAAGAAGAAGGAAGAGGAAAAGGATGGTATGCCGGAATTGGAGGACTGGGCTGGATCCATG

ORF - retro_tsyr_1453 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.03 %
Parental protein coverage: 86.25 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHD-NMDIDKVDELMQDIADQQELAEEISTAISKP-VG
ST..F.REA..........L...G.AA.A.KA......DIDK.D.L....A..QELAE......S.P..G
RetrocopySTPAFEREA*A-CQPGAQALRGVGCAAVATKATGG<SADIDKADVLLRAAAHPQELAE----VVSRP<FG
ParentalFGEEFDEDELMAELEELEQE-ELDKNLLEISGPETVPLPNVPSIALPSKPAKKKEEEDDDMKELENWAGS
FGE.F.EDELMA.LE.LEQ..ELDK...E.SGPE.V..PNV.SI.LPSK.AKKKEEE.D.M.ELE.WAGS
RetrocopyFGEDFEEDELMAGLEDLEQV<ELDKD*METSGPEPVLPPNVLSIGLPSKHAKKKEEEKDGMPELEDWAGS
ParentalM
M
RetrocopyM

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






RNA-Seq - click to see more details

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tarsius syrichta was not studied using ChIP-Seq data.

EST - click to see more details

Tarsius syrichta was not studied using EST data.

TSS - click to see more details

Tarsius syrichta was not studied using FANTOM5 data.

Lab - click to see more details

retro_tsyr_1453 was not experimentally validated.

Retrocopy orthology:
Tarsius syrichta 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 15 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000090381 retrocopy
retro_amel_1612,
Canis familiaris ENSCAFG000000074781 retrocopy
retro_cfam_1304,
Choloepus hoffmanni ENSCHOG000000072881 retrocopy
retro_chof_2518,
Equus caballus ENSECAG000000083111 retrocopy
retro_ecab_496,
Felis catus ENSFCAG000000258931 retrocopy
retro_fcat_1835,
Homo sapiens ENSG000001014211 retrocopy
retro_hsap_1339,
Gorilla gorilla ENSGGOG000000077751 retrocopy
retro_ggor_29,
Macaca mulatta ENSMMUG000000080841 retrocopy
retro_mmul_2178,
Mustela putorius furoENSMPUG000000178212 retrocopies
retro_mputfur_1302, retro_mputfur_697,
Nomascus leucogenys ENSNLEG000000100201 retrocopy
retro_nleu_1822,
Pongo abelii ENSPPYG000000109311 retrocopy
retro_pabe_1111,
Pan troglodytes ENSPTRG000000134081 retrocopy
retro_ptro_915,
Pteropus vampyrus ENSPVAG000000102931 retrocopy
retro_pvam_973,
Rattus norvegicus ENSRNOG000000465851 retrocopy
retro_rnor_61,
Tarsius syrichta ENSTSYG00000013212 1 retrocopy
retro_tsyr_1453 ,


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