RetrogeneDB ID: retro_vpac_642

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_91384:499..1085(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC109B
• Ensembl ID: ENSVPAG00000009837
• Aliases: None
• Description: coiled-coil domain containing 109B [Source:HGNC Symbol;Acc:26076]

Sequence

>retro_vpac_642
CAAGACAAAGGTAACAAAACCGCCGCCGTCTTCACAGCAGATGGCAGTGAAACTGCAGCTTCAACCTTGATGGAAGTTTT
GCTAATGAATGCTTTTAAACTTGTCATTAATAAAATAACATATGCCGTGCAGTGCGCCAAGAAAGAAAAACTGAGTCGTG
AGCCGACTAACGAGATGGAAAGCATGAACTCCTTGGTTCACAGACTGCGCACAGACTTGCATTTGGAAGTTTCAGAAAAA
GAAAGCGCACCATCTGCTGGAGAAAACTGAGCACCTGAAGGGACAGCTGCGGCCCTTTGAGCAGATGAAAGCCACAACAG
AAGCTCGTTCAGAAGCCACAACCAGTGGCCTCCTGTGGGCTGGGCTCGCGCTGCTGTGTGTTCAGGGCAGGGCAGTGGCC
TGGCTCACTTGGTGGGTGTCCTCCTGGGATATTGCGGGACCAGTTACATACTTCATCACATTTGCAAATTGCATGGTCCT
TTTTGCATACTTTATAGTCACTCGACAGGATTATACTCACTCAGCTGTTAAGAGCAGGCAGTTTCTTCACTTCTTCGGTA
AGAAATCAAAACAACATGGTTTTGAT

Alignment

ORF - retro_vpac_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.8 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDKGIKTAAIFTADGSEIAASTLMEVLLMNDFKLVINKITYDVQCPKKEKLSREQTTEMENMKSLVHRLF
          .DKG.KTAA.FTADGSE.AASTLMEVLLMN.FKLVINKITY.VQC.KKEKLSRE.T.EME.M.SLVHRL.
Retrocopy QDKGNKTAAVFTADGSETAASTLMEVLLMNAFKLVINKITYAVQCAKKEKLSREPTNEMESMNSLVHRLR

Parental  TALHLE-EFQK-KREHHLLEKIDHLKGQLQPLEQM-AKIEDRSEAKTSGLLWAGLALLSVQGGAMAWLTW
          T.LHLE..F.K.K..HHLLEK..HLKGQL.P.EQM.A..E.RSEA.TSGLLWAGLALL.VQG.A.AWLTW
Retrocopy TDLHLE<SFRK<KKAHHLLEKTEHLKGQLRPFEQMKATTEARSEATTSGLLWAGLALLCVQGRAVAWLTW

Parental  WVYSWDIMEPVTYFITFANSMVFFAYFIVTRQDYTYSAVKSRQFLHFFHKKSKQQHFD
          WV.SWDI..PVTYFITFAN.MV.FAYFIVTRQDYT.SAVKSRQFLHFF.KKSKQ..FD
Retrocopy WVSSWDIAGPVTYFITFANCMVLFAYFIVTRQDYTHSAVKSRQFLHFFGKKSKQHGFD

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_642 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_642 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.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013586	1 retrocopy	retro_etel_443,
Loxodonta africana	ENSLAFG00000002726	1 retrocopy	retro_lafr_1127,
Ochotona princeps	ENSOPRG00000017044	1 retrocopy	retro_opri_646,
Vicugna pacos	ENSVPAG00000009837	1 retrocopy	retro_vpac_642 ,