RetrogeneDB ID:

retro_vpac_422

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_17554:6405..6732(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHMP1B
Ensembl ID:ENSVPAG00000000854
Aliases:None
Description:charged multivesicular body protein 1B [Source:HGNC Symbol;Acc:24287]


Retrocopy-Parental alignment summary:






>retro_vpac_422
AAACACCTGTTCAACCTGAAGTTCGCGGCCAAAGAACTGAGCAGGAGTGCCAAAAAATGCGACAAGGAGGAAAAGGCTGA
GAAGGCCAAAATTAAGAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATTCACGCCGAGAATGCGATTCGCCAGA
AGAACCAGGCGGTGAATTTCCTGAGAATGAGCGCGCGGGTCGACGCGGTGGCCGCCAGGGTCCAGACGGCCGTGACGATG
GGCAAGGTGACCAAGTCTATGGCCGGTGTGGTGAAGTCGATGGACGCGACGCTGAAGACCATGAATCTGGAGAAGATCTC
CGCCCTG

ORF - retro_vpac_422 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.14 %
Parental protein coverage: 55.5 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalEHLFNLKFAAKELNRNAKKCDKEEKAEKAKIKSLKQAIQKGNTEVARIHAENAIRQKNQAINFLRMSARV
.HLFNLKFAAKEL.R.AKKCDKEEKAEKAKI...K.AIQKGN.EVARIHAENAIRQKNQA.NFLRMSARV
RetrocopyKHLFNLKFAAKELSRSAKKCDKEEKAEKAKI---KKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARV
ParentalDAVAARVQTAVTMGKV-NSQRCVVKSMDVTLRSRTLKKISAL
DAVAARVQTAVTMGKV..S...VVKSMD.TL....L.KISAL
RetrocopyDAVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISAL

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






RNA-Seq - click to see more details

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Vicugna pacos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_vpac_422 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_422 was not experimentally validated.

Retrocopy orthology:
Vicugna pacos 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 26 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000266601 retrocopy
retro_cpor_1434,
Equus caballus ENSECAG000000186251 retrocopy
retro_ecab_991,
Gorilla gorilla ENSGGOG000000256041 retrocopy
retro_ggor_1368,
Loxodonta africana ENSLAFG000000264572 retrocopies
retro_lafr_214, retro_lafr_826,
Macropus eugenii ENSMEUG000000152502 retrocopies
retro_meug_1196, retro_meug_205,
Myotis lucifugus ENSMLUG000000248113 retrocopies
retro_mluc_1161, retro_mluc_1344, retro_mluc_673,
Monodelphis domestica ENSMODG000000042732 retrocopies
retro_mdom_1444, retro_mdom_154,
Mus musculus ENSMUSG000000312421 retrocopy
retro_mmus_1735,
Ochotona princeps ENSOPRG000000185561 retrocopy
retro_opri_577,
Pongo abelii ENSPPYG000000205051 retrocopy
retro_pabe_1581,
Pteropus vampyrus ENSPVAG000000014162 retrocopies
retro_pvam_208, retro_pvam_59,
Rattus norvegicus ENSRNOG000000023232 retrocopies
retro_rnor_1361, retro_rnor_623,
Sarcophilus harrisii ENSSHAG000000169032 retrocopies
retro_shar_776, retro_shar_778,
Tarsius syrichta ENSTSYG000000117271 retrocopy
retro_tsyr_1611,
Tursiops truncatus ENSTTRG000000080662 retrocopies
retro_ttru_1002, retro_ttru_235,
Vicugna pacos ENSVPAG00000000854 2 retrocopies
retro_vpac_112, retro_vpac_422 ,


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