RetrogeneDB ID: retro_vpac_500

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_258279:94..856(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC91
• Ensembl ID: ENSVPAG00000009241
• Aliases: None
• Description: coiled-coil domain containing 91 [Source:HGNC Symbol;Acc:24855]

Sequence

>retro_vpac_500
GGTAGAGCTTCGCTGACGTTGCCACTGATGCCAAAGTGGAATAAAGTAGCTGGAGTCCATCTTGCCCCCAGCTTCTCCTG
AAATTGTACTGGACCATGACCACACTTCTCCTTCTGTTGGCTCCTCTCTTCTGAGCCCATCATTTCCTCGCCAGAGAATA
CACATACAGACAACAGCATTGTCAGTCAGACGGTTCTTAAAGCACAGATTCAGCAATCAACACACACTCATCTGGATATC
TCATTTTTTCCACTGGGTTTAACTGAGGAGAAAAGTAATGGAACAATTGCTCCTGTGGGTGATTCTGAGGATCCTGGAGC
CAACGTATCAAACATACAGCTTCAGCAGAAAATTGCAAGTCTGGAGATGAAACTCAAAAGTTTCTGAAGAAGAAAAACAG
AGAATTAAAGAGGATGTGGAATCATTGATGGAAAAACATAGTGTCTCAGAAAAAGATTCCCTTAAAGAAAAAGAGCAAGA
GGCCATTTCTTTTCAAGATAGATACAAAGAACTTCAGGAAAAACATAAACAAGAATTAGAAGACATGAGGGAAGCTGGTC
ATGAGCCCTCAGCATCATTGTGGATTAATATAAGGCACTACTGCAGTCTTCAGTTAAGCAACAAGTAGAAGCAATTGAAA
AACAGTACATTTCTGCAACTGAGAAACAAGCACACAAGTGTGAGGAGTTGTTAAATACTCAGCATCAGCGGCTGCTTGAA
ATGCTAGATACAGAGAAGGAACTGTTAAAAGAAAAAAATAAG

Alignment

ORF - retro_vpac_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.31 %
• Parental protein coverage: 57.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GETQTTSPAIPWAAFPTVAGVHLSP-ASPEIVLDHDHSSPSVGC-LSSEPIISSPENTHADNSIVGQTVP
          G....T.P..P......VAGVHL.P.ASPEIVLDHDH.SPSVG..LSSEPIISSPENTH.DNSIV.QTV.
Retrocopy GRASLTLPLMP--KWNKVAGVHLAP>ASPEIVLDHDHTSPSVGS<LSSEPIISSPENTHTDNSIVSQTVL

Parental  KAQIQQSTHTHLDISLFPLGLTDEKSNGTIAPVGDSEDPGANVSNIQLQQKIASLEMKLK-VSEEEKQRI
          KAQIQQSTHTHLDIS.FPLGLT.EKSNGTIAPVGDSEDPGANVSNIQLQQKIASLEMKLK.VSEEEKQRI
Retrocopy KAQIQQSTHTHLDISFFPLGLTEEKSNGTIAPVGDSEDPGANVSNIQLQQKIASLEMKLK>VSEEEKQRI

Parental  KKDVESLMEKHSVLEKDFLKEKEQEAISFQDRYKELQEKHKQELEDMRKAGHE-ALSIIVDEYKALLQSS
          K.DVESLMEKHSV.EKD.LKEKEQEAISFQDRYKELQEKHKQELEDMR.AGHE.ALSIIVD.YKALLQSS
Retrocopy KEDVESLMEKHSVSEKDSLKEKEQEAISFQDRYKELQEKHKQELEDMREAGHE<ALSIIVD*YKALLQSS

Parental  VKQQVEAIEKQYISAIEKQAHKCEELLNTQHQRLLEMLDTEKELLKGKIK
          VKQQVEAIEKQYISA.EKQAHKCEELLNTQHQRLLEMLDTEKELLK.K.K
Retrocopy VKQQVEAIEKQYISATEKQAHKCEELLNTQHQRLLEMLDTEKELLKEKNK

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_500 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_500 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000009241	1 retrocopy	retro_vpac_500 ,