RetrogeneDB ID:

retro_vpac_442

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_1966:145120..145468(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM2
Ensembl ID:ENSVPAG00000009286
Aliases:None
Description:calmodulin 2 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1445]


Retrocopy-Parental alignment summary:






>retro_vpac_442
GGAACTGTCATGTGCTCACTGGGTCAGAACTCAACAGAAGCCAAATAGCAGGGTATGATCAACGAAGTGGATGCTGATGG
CAATGGCACCATTGACTTCCCAGAGTTTTTGACTATGATGGCTAGAAAAATGAAAGATACAGACAGTGAAGAAGAAATCT
GTGAGGCATTCTGAGTCTTTGACAAGGATGGCAGTGGTTACATCAGTGCTGCAAAACTACATCACATCATGACAAACTTA
GGAGAAAAACTAACAGATGAGGAAGTAGATGAAATGAACAGAGAAACAGAGATTGATGGAGATGGACAAGTCAACTACAA
AAAATTTGTACAGATGATGACCGCAAAG

ORF - retro_vpac_442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.21 %
Parental protein coverage: 77.85 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISA
GTVM.SLGQN.TEA..Q.MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEI.EAF.VFDKDG.GYISA
RetrocopyGTVMCSLGQNSTEAK*QGMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEICEAF*VFDKDGSGYISA
ParentalAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
A.L.H.MTNLGEKLTDEEVDEM.RE..IDGDGQVNY..FVQMMTAK
RetrocopyAKLHHIMTNLGEKLTDEEVDEMNRETEIDGDGQVNYKKFVQMMTAK

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_442 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_442 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 19 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000157121 retrocopy
retro_acar_45,
Choloepus hoffmanni ENSCHOG000000082456 retrocopies
retro_chof_1940, retro_chof_2261, retro_chof_367, retro_chof_735, retro_chof_833, retro_chof_965,
Cavia porcellus ENSCPOG000000121813 retrocopies
retro_cpor_1012, retro_cpor_87, retro_cpor_89,
Echinops telfairi ENSETEG000000093775 retrocopies
retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Ficedula albicollis ENSFALG000000128281 retrocopy
retro_falb_16,
Gadus morhua ENSGMOG000000093421 retrocopy
retro_gmor_23,
Latimeria chalumnae ENSLACG000000050591 retrocopy
retro_lcha_53,
Loxodonta africana ENSLAFG000000098651 retrocopy
retro_lafr_655,
Myotis lucifugus ENSMLUG000000290166 retrocopies
retro_mluc_13, retro_mluc_1732, retro_mluc_18, retro_mluc_19, retro_mluc_2207, retro_mluc_2258,
Macaca mulatta ENSMMUG000000174661 retrocopy
retro_mmul_256,
Monodelphis domestica ENSMODG000000092221 retrocopy
retro_mdom_1126,
Otolemur garnettii ENSOGAG000000088246 retrocopies
retro_ogar_1126, retro_ogar_1196, retro_ogar_1432, retro_ogar_1535, retro_ogar_209, retro_ogar_2326,
Petromyzon marinus ENSPMAG000000033231 retrocopy
retro_pmar_12,
Pongo abelii ENSPPYG000000124305 retrocopies
retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599,
Pelodiscus sinensis ENSPSIG000000131731 retrocopy
retro_psin_9,
Sus scrofa ENSSSCG000000084331 retrocopy
retro_sscr_228,
Taeniopygia guttata ENSTGUG000000025811 retrocopy
retro_tgut_6,
Vicugna pacos ENSVPAG000000045631 retrocopy
retro_vpac_472,
Vicugna pacos ENSVPAG00000009286 1 retrocopy
retro_vpac_442 ,


Copyright © RetrogeneDB 2014-2017