RetrogeneDB ID:

retro_vpac_126

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_1966:766050..766332(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IMMP1L
Ensembl ID:ENSVPAG00000001940
Aliases:None
Description:IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae) [Source:HGNC Symbol;Acc:26317]


Retrocopy-Parental alignment summary:






>retro_vpac_126
AATCCAAGTGATTCAAAATTAAACGTTGGTAAAAGAGTCATTGGTTTGAAAGGAGGCAAAAGCTGCAGCAATAGTCCATC
AGACTTCTTTAAAAAGCCATAGTTATGTGCCAGCGGATCACTTTGGTGAGAAGGTGATAATCTGCAGGTCACTGCAGATT
GCAGGTGTTGTGGACCTATTCCCTGCGGACTAATAAGAGAATGTATCTTCTTTAAGATTTGGCCTCTGAGTGACGTTGGA
TTTCCACCTGAAGGCCTTAATGGCCACAGATTTTATAATGAC

ORF - retro_vpac_126 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.62 %
Parental protein coverage: 56.63 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSPSDPKSNICKRVIGLEGDKILSNSPSDFFK-SHSYVPTGH-VWLEGDNLQNSTDSRYYGPVPYGLIRGR
.PSD.K.N..KRVIGL.G.K..SNSPSDFFK.SHSYVP..H..W.EGDNLQ...D.R..GP.P.GLIR..
RetrocopyNPSDSKLNVGKRVIGLKGGKSCSNSPSDFFK>SHSYVPADH<LW*EGDNLQVTADCRCCGPIPCGLIREC
ParentalIFFKIWPLSDFGFLRDSPNGHRFSDD
IFFKIWPLSD.GF.....NGHRF..D
RetrocopyIFFKIWPLSDVGFPPEGLNGHRFYND

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_126 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_126 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 27 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068761 retrocopy
retro_amel_623,
Bos taurus ENSBTAG000000004751 retrocopy
retro_btau_528,
Canis familiaris ENSCAFG000000075142 retrocopies
retro_cfam_1757, retro_cfam_548,
Choloepus hoffmanni ENSCHOG000000101064 retrocopies
retro_chof_1157, retro_chof_1665, retro_chof_2427, retro_chof_358,
Callithrix jacchus ENSCJAG000000060421 retrocopy
retro_cjac_1240,
Dipodomys ordii ENSDORG000000002504 retrocopies
retro_dord_144, retro_dord_205, retro_dord_243, retro_dord_726,
Equus caballus ENSECAG000000205123 retrocopies
retro_ecab_1019, retro_ecab_159, retro_ecab_920,
Echinops telfairi ENSETEG000000030571 retrocopy
retro_etel_1971,
Homo sapiens ENSG000001489501 retrocopy
retro_hsap_786,
Gorilla gorilla ENSGGOG000000148971 retrocopy
retro_ggor_651,
Myotis lucifugus ENSMLUG000000065042 retrocopies
retro_mluc_2105, retro_mluc_385,
Macaca mulatta ENSMMUG000000168061 retrocopy
retro_mmul_1092,
Mus musculus ENSMUSG000000426702 retrocopies
retro_mmus_2571, retro_mmus_591,
Nomascus leucogenys ENSNLEG000000178821 retrocopy
retro_nleu_2484,
Oryctolagus cuniculus ENSOCUG000000296121 retrocopy
retro_ocun_388,
Otolemur garnettii ENSOGAG000000078533 retrocopies
retro_ogar_1202, retro_ogar_2006, retro_ogar_2643,
Pongo abelii ENSPPYG000000033891 retrocopy
retro_pabe_747,
Pan troglodytes ENSPTRG000000034721 retrocopy
retro_ptro_547,
Pteropus vampyrus ENSPVAG000000155351 retrocopy
retro_pvam_932,
Rattus norvegicus ENSRNOG000000048291 retrocopy
retro_rnor_2450,
Sarcophilus harrisii ENSSHAG000000154072 retrocopies
retro_shar_396, retro_shar_491,
Sus scrofa ENSSSCG000000133221 retrocopy
retro_sscr_1178,
Ictidomys tridecemlineatus ENSSTOG000000031792 retrocopies
retro_itri_489, retro_itri_623,
Tupaia belangeri ENSTBEG000000021266 retrocopies
retro_tbel_1510, retro_tbel_2503, retro_tbel_315, retro_tbel_3504, retro_tbel_4049, retro_tbel_878,
Tarsius syrichta ENSTSYG000000092571 retrocopy
retro_tsyr_2139,
Tursiops truncatus ENSTTRG000000023952 retrocopies
retro_ttru_1862, retro_ttru_966,
Vicugna pacos ENSVPAG00000001940 1 retrocopy
retro_vpac_126 ,




Copyright © RetrogeneDB 2014-2017