RetrogeneDB ID: retro_vpac_400

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_15843:3797..4176(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSVPAG00000000595
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_vpac_400
GCATCTGATGCCCAGGCAGTGGCTGATGCAGTCATTTTTCAGCTTGGTTTCCACAGCATTGAGCTGAATAAGCCTCCACT
AGTATACATGGCAGCCAGCCTCTTTAAGGAGATAGGTTACTGATACCAGGAAGACCTGATGGCAGCAATCATCATTGTGG
GCTGGGACCCCCAAGAAGGGGTGCATATGTACTCAGGGCCCATGGTGGGGTATGATAGTAAGACAGTCCTTTGCCACTGG
GGGCTCTGGGAGCTCCTGTATCTATGACTATTTCGATGCTACCTACTGGGAATGCATGACCAAGGAAAAGTGTCTGCAAT
TCGCTGCTAGTGCTCTCCCTTTGGCCATGGAGCAGGACTGCTCCAGTGGAGGGTTGGTC

Alignment

ORF - retro_vpac_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 63.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCCRYREDLMAGIIIAGWDPQEGGQKYSVPM-G
          A.D.QAVADAV..QLGFHSIELN.PPLV..AASLFKE....Y.EDLMA.III.GWDPQEG...YS.PM..
Retrocopy ASDAQAVADAVIFQLGFHSIELNKPPLVYMAASLFKEIGY*YQEDLMAAIIIVGWDPQEGVHMYSGPM>W

Parental  GMMVRQSFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVI
          GM.VRQSFA.GGSGSS.IY.Y.DATY.E.MTKE.CLQF.A.AL.LAME.D.SSGG..
Retrocopy GMIVRQSFATGGSGSSCIYDYFDATYWECMTKEKCLQFAASALPLAMEQDCSSGGLV

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_400 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_400 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000005851	1 retrocopy	retro_dord_613,
Erinaceus europaeus	ENSEEUG00000002083	3 retrocopies	retro_eeur_203, retro_eeur_607, retro_eeur_71,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Vicugna pacos	ENSVPAG00000000595	1 retrocopy	retro_vpac_400 ,