RetrogeneDB ID:

retro_chof_2419

Retrocopy
location
Organism:Sloth (Choloepus hoffmanni)
Coordinates:scaffold_73828:4735..5093(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PDPN
Ensembl ID:ENSCHOG00000007003
Aliases:None
Description:podoplanin [Source:HGNC Symbol;Acc:29602]


Retrocopy-Parental alignment summary:






>retro_chof_2419
CAGCATGGTCTGACCATTTTTCCAGGTGTGGAAAAATGGCATGGTGACTCCAGGTGCCAGTGAAGAGCCCAGTAATTCTG
CTGGCTTGACAATTCTGGGGCCAAAAAGGGCAAAGAGAGTGACAGTCATTCTCATGAAGGGTTGGTCATCTATAGAAAGC
ACATTCCATGCCCAAGAAGAAAGTCAGAACACCACAGCCCCAAATGCAGTGAGTGGTCACTCTGGGAAACTGGGTAGAGA
GGCACCATCAAGAGTTGAGAACAATGGTTTGGCAATAGTAACCCTGATTGGAATCATAGTTGGGGTCTTACTAGCCATTG
GTTTCATTGGTGCAGTCATCATTGTGGTTGTGCAAAAA

ORF - retro_chof_2419 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.83 %
Parental protein coverage: 84.56 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEDGAAVSPGVE-DGVVTPGASEQPDKSAGLTTQGLTTTKSVTVIRVTDRTPLEST----EESQKTTASNV
..G....PGVE..G.VTPGASE.P..SAGLT..G....K.VTVI........EST....EESQ.TTA.N.
RetrocopyQHGLTIFPGVE>NGMVTPGASEEPSNSAGLTILGPKRAKRVTVILMKGWSSIESTFHAQEESQNTTAPNA
ParentalGTGHSEKVGGEALPTVENDGLTTVTLVGIIVGVSLATAFIGGVIYMVVRK
..GHS.K.G.EA...VEN.GL..VTL.GIIVGV.LA..FIG.VI..VV.K
RetrocopyVSGHSGKLGREAPSRVENNGLAIVTLIGIIVGVLLAIGFIGAVIIVVVQK

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






Choloepus hoffmanni was not studied using RNA-Seq expression data.
Choloepus hoffmanni was not studied using ChIP-Seq data.
Choloepus hoffmanni was not studied using EST data.
Choloepus hoffmanni was not studied using FANTOM5 data.
retro_chof_2419 was not experimentally validated.

Retrocopy orthology:
Choloepus hoffmanni 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 5 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG00000007003 3 retrocopies
retro_chof_1612, retro_chof_2419 , retro_chof_583,
Callithrix jacchus ENSCJAG000000137721 retrocopy
Mus musculus ENSMUSG000000285831 retrocopy
Pteropus vampyrus ENSPVAG000000111801 retrocopy
Tarsius syrichta ENSTSYG000000056671 retrocopy



Copyright © RetrogeneDB 2014-2017