RetrogeneDB ID: retro_vpac_478

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_236133:38..574(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PIGF
• Ensembl ID: ENSVPAG00000000314
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class F [Source:HGNC Symbol;Acc:8962]

Sequence

>retro_vpac_478
ATGAAAGATGCTGACTTCAAGAGACTACTGTGTGCCTATCTTTTATGCATATTTTCAATGATCCTCGGCATCGTCATTTC
ATCATTCCTCTTGGAGAACTTTGCAATATTGGAAACACACTGGACATGGTCATGCACCTGTTCTGTTTTGGTAACTGCTG
TCACCTTAGTATTACACTGAGTGGTGAAACCAACTGCATCTCTCAAAGAAGTTCATTATCACAAGGTCACCAGCCTTTTG
AAATGCTGTATCAACTTTCTTATGTCTTGTTTCCCCTTTCCGGTAATTTTTGTTCTGTATGGAGCACCACTAATCAAGTT
GGTGTTGGAAACGTTTTCCTTTGCAGTTCGCTGGTCTACTTTTACTACTGTACCCTGTTCATGTTTGTTAGGACCAAACT
TCAAAGCAGGTCTAAGAGTTTTCTATAGAAGCGGGGTCACATCCATTGGCAGAAGAGTCTCTCGATCATTATGGTTTCTA
GTTTTGTAGGAACAAGGCTTGGGGACTTTCCTTTTCCACTTGATTGGGGAAGACCG

Alignment

ORF - retro_vpac_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.61 %
• Parental protein coverage: 82.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKDTDIKRLLYAHLVCIFSIILSIFIPSFFLENFSILETHLTWLCICSVFVTAVNLILYLVGKPNTSSKR
          MKD.D.KRLL.A.L.CIFS.IL.I.I.SF.LENF.ILETH.TW.C.CSV.VTAV.L.L..V.KP..S.K.
Retrocopy MKDADFKRLLCAYLLCIFSMILGIVISSFLLENFAILETHWTWSCTCSVLVTAVTLVLH*VVKPTASLKE

Parental  SSLSYKVTRLLKCYIYFLMSCFSFHVIFVLYGAPLTELVLETFSLAVLLSTFTTVPCLCLLGPNFKAWLR
          .....KVT.LLKC.I.FLMSCF.F.VIFVLYGAPL..LVLETFS.AV..STFTTVPC.CLLGPNFKA.LR
Retrocopy VHY-HKVTSLLKCCINFLMSCFPFPVIFVLYGAPLIKLVLETFSFAVRWSTFTTVPCSCLLGPNFKAGLR

Parental  VFSRNGATSI-WENSLQITTISSIVGTWLGAFPIPLDWGRP
          VF.R.G.TSI.W..SL.I...SS.VGT.LG.FP.PLDWGRP
Retrocopy VFYRSGVTSI<WQKSLSIIMVSSFVGTRLGDFPFPLDWGRP

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_478 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_478 was not experimentally validated.

Homology

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 20 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028483	1 retrocopy	retro_acar_103,
Callithrix jacchus	ENSCJAG00000000680	2 retrocopies	retro_cjac_4146, retro_cjac_481,
Dasypus novemcinctus	ENSDNOG00000007278	2 retrocopies	retro_dnov_1980, retro_dnov_502,
Dasypus novemcinctus	ENSDNOG00000025474	1 retrocopy	retro_dnov_602,
Dipodomys ordii	ENSDORG00000006083	1 retrocopy	retro_dord_234,
Homo sapiens	ENSG00000151665	3 retrocopies	retro_hsap_3277, retro_hsap_4217, retro_hsap_4801,
Gorilla gorilla	ENSGGOG00000024478	3 retrocopies	retro_ggor_2229, retro_ggor_2825, retro_ggor_2988,
Myotis lucifugus	ENSMLUG00000008686	1 retrocopy	retro_mluc_1471,
Macaca mulatta	ENSMMUG00000005389	2 retrocopies	retro_mmul_1173, retro_mmul_2559,
Monodelphis domestica	ENSMODG00000000968	1 retrocopy	retro_mdom_1771,
Mustela putorius furo	ENSMPUG00000012037	1 retrocopy	retro_mputfur_810,
Nomascus leucogenys	ENSNLEG00000016924	3 retrocopies	retro_nleu_1115, retro_nleu_1455, retro_nleu_2882,
Oryctolagus cuniculus	ENSOCUG00000001130	1 retrocopy	retro_ocun_618,
Otolemur garnettii	ENSOGAG00000026734	1 retrocopy	retro_ogar_1699,
Pongo abelii	ENSPPYG00000012438	3 retrocopies	retro_pabe_2710, retro_pabe_3450, retro_pabe_3733,
Pan troglodytes	ENSPTRG00000011895	2 retrocopies	retro_ptro_2863, retro_ptro_3192,
Ictidomys tridecemlineatus	ENSSTOG00000001373	1 retrocopy	retro_itri_989,
Tupaia belangeri	ENSTBEG00000000891	1 retrocopy	retro_tbel_3809,
Tarsius syrichta	ENSTSYG00000002842	3 retrocopies	retro_tsyr_1497, retro_tsyr_1556, retro_tsyr_1820,
Vicugna pacos	ENSVPAG00000000314	1 retrocopy	retro_vpac_478 ,