RetrogeneDB ID:

retro_vpac_644

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_919:424259..424733(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CFL2
Ensembl ID:ENSVPAG00000003273
Aliases:None
Description:cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]


Retrocopy-Parental alignment summary:






>retro_vpac_644
AGCTCAGGAGTTACAGTGAATGATGACATCACCAGAGTTTTTCACGATAAGAAAATAAGGAAATCTACACAAGAGGAGAT
CAAAAAAAGAAATAAAACTGTTATCTTCTGTTTAAGGGGAGAGAAAAAGACTGAAAAGGAAGCAAAGCAGATCTTGGGGA
ATGACACTGGTGATACTGCAGAGGATCCCTATACATCTGTTGTGACGTTGGTACCTCCAAATGATTGCTAATCGGCTCTG
TATGATGCCACATGAGAAACAGAAGAGTCCAAGAAAGAATTTATATTCTGGGCTTCTGAGAGTGCACCTTTAAAAAGCAA
GATTATTTATGTCAGCTTTAAAGATGTCATTAAAAAGAAATTTGGAGATATTAAACATGAGTGGCATGTAAATGGCATGG
ATGACATAATGAAGCATTCACCACTTGGAGAGAACTTGGGAGACAATGCAGTAGTCTCACTTGAAGGAAAACCC

ORF - retro_vpac_644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.29 %
Parental protein coverage: 98.8 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalASGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPYTSF
.SGVTVND....VF.D.K.RKS.TQEEIKKR.K.V.FCL...K......EAKQIL..D.GDT.EDPYTS.
RetrocopySSGVTVNDDITRVFHDKKIRKS-TQEEIKKRNKTVIFCLRGEKKT--EKEAKQILGNDTGDTAEDPYTSV
ParentalVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLD
V.L.P.NDC..ALYDAT.ET.ESKKE...FIFWA.ESAPLKSK.IY.S.KD.IKKKF..IKHEW.VNG.D
RetrocopyVTLVPPNDC*SALYDAT*ETEESKKE---FIFWASESAPLKSKIIYVSFKDVIKKKFGDIKHEWHVNGMD
ParentalDIKDRSTLGEKLGGNVVVSLEGKP
DI...S.LGE.LG.N.VVSLEGKP
RetrocopyDIMKHSPLGENLGDNAVVSLEGKP

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_644 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_644 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 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000155081 retrocopy
retro_amel_1347,
Canis familiaris ENSCAFG000000325621 retrocopy
retro_cfam_1006,
Cavia porcellus ENSCPOG000000089961 retrocopy
retro_cpor_1003,
Echinops telfairi ENSETEG000000060103 retrocopies
retro_etel_1579, retro_etel_1622, retro_etel_684,
Felis catus ENSFCAG000000084802 retrocopies
retro_fcat_1223, retro_fcat_1395,
Latimeria chalumnae ENSLACG000000180111 retrocopy
retro_lcha_23,
Loxodonta africana ENSLAFG000000105791 retrocopy
retro_lafr_1041,
Macropus eugenii ENSMEUG0000000073911 retrocopies
retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Microcebus murinus ENSMICG000000092371 retrocopy
retro_mmur_493,
Monodelphis domestica ENSMODG000000129491 retrocopy
retro_mdom_171,
Mus musculus ENSMUSG000000629291 retrocopy
retro_mmus_660,
Otolemur garnettii ENSOGAG000000323211 retrocopy
retro_ogar_2346,
Pteropus vampyrus ENSPVAG000000027981 retrocopy
retro_pvam_398,
Rattus norvegicus ENSRNOG000000458921 retrocopy
retro_rnor_684,
Sarcophilus harrisii ENSSHAG000000047321 retrocopy
retro_shar_528,
Sus scrofa ENSSSCG000000019592 retrocopies
retro_sscr_1198, retro_sscr_327,
Ictidomys tridecemlineatus ENSSTOG000000016753 retrocopies
retro_itri_1313, retro_itri_581, retro_itri_632,
Tupaia belangeri ENSTBEG000000003912 retrocopies
retro_tbel_29, retro_tbel_4131,
Vicugna pacos ENSVPAG00000003273 1 retrocopy
retro_vpac_644 ,


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