RetrogeneDB ID: retro_vpac_166

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2320:1277482..1277717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGP
• Ensembl ID: ENSVPAG00000009781
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class P [Source:HGNC Symbol;Acc:3046]

Sequence

>retro_vpac_166
AGAATGTGCCAAGTCACAAGGACAACGGTAGAAAATTCACCGTTGGCTGTCACCGGAAAGAGCAATCCATAAACGCTCTG
TTCTTTTCTTAACCTCCCACTCTGGCATCATGCTATAGTGCATGCAGGCTTTTATTCCTAAATCGTGGCTAAACTACTTA
GTCTTAAATGATTGGCCTCAAAAATATTGGGCAGGTGCATTACCTGTCTACTTCTTTATAGCTGTAGTAATCGGC

Alignment

ORF - retro_vpac_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.96 %
• Parental protein coverage: 66.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLSKATGKMVENSPSPL-PERAIYG-FVLFLSSRFGFILYLVWAFIPESWLNSLGLTYWPQKYWAVALPV
          R....T...VENSP....PERAI....VLFL.S..G..L....AFIP.SWLN.L.L..WPQKYWA.ALPV
Retrocopy RMCQVTRTTVENSPLAV>PERAIHKRSVLFLTSHSGIML*CMQAFIPKSWLNYLVLNDWPQKYWAGALPV

Parental  YLLITIVIG
          Y..I..VIG
Retrocopy YFFIAVVIG

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_166 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_166 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 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009702	4 retrocopies	retro_cfam_1022, retro_cfam_1559, retro_cfam_1976, retro_cfam_238,
Myotis lucifugus	ENSMLUG00000005475	3 retrocopies	retro_mluc_1419, retro_mluc_1444, retro_mluc_2084,
Monodelphis domestica	ENSMODG00000020988	1 retrocopy	retro_mdom_1807,
Mustela putorius furo	ENSMPUG00000008312	5 retrocopies	retro_mputfur_1069, retro_mputfur_1388, retro_mputfur_421, retro_mputfur_642, retro_mputfur_826,
Sarcophilus harrisii	ENSSHAG00000014284	1 retrocopy	retro_shar_548,
Tupaia belangeri	ENSTBEG00000001803	4 retrocopies	retro_tbel_1750, retro_tbel_2361, retro_tbel_3162, retro_tbel_655,
Tursiops truncatus	ENSTTRG00000007711	3 retrocopies	retro_ttru_1043, retro_ttru_677, retro_ttru_883,
Vicugna pacos	ENSVPAG00000009781	3 retrocopies	retro_vpac_166 , retro_vpac_387, retro_vpac_639,