RetrogeneDB ID: retro_vpac_456

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_21124:726..1222(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3A
• Ensembl ID: ENSVPAG00000004995
• Aliases: None
• Description: general transcription factor IIIA [Source:HGNC Symbol;Acc:4662]

Sequence

>retro_vpac_456
CTTTGTGCAGCTAGCCTCTGTGCTCATAAATGCCACACAAAATCAAACCTGAGGAAACACTTGATAAGCAAACATGAAAA
CCAGCCAAAACAATACGTAGGCAGTTCTGAAGGTTGTGAGACCTTTCAGAAACATCTGCAGCTGAAAATCCATCAGTACC
AGCAAAACAACGAGCACTGTTCAGGTGTACCCAAGGCTGTGGAAAACACGTCACTTACCCTCCCCCCCCTCCCTGGCGAC
ACCCGAAGATCCAGGAGGACTATGTATTTCAAAGAGAATGTTCTTTTGCGGCAAAAACATGGACGAAGATTCTAAACGTG
AGAGAAACTCATAAAGCGGAAACAATATGTGACACGAGCGGGAAAACATTTTAACTTGAAGCTTACCTTAGGCGACACAT
GAAAACTCAGGTCCCAGACAGAGACGTAGCCGCTGTCGGACAGAAGGCTGTGGCCGGACGGCCACCGCCGCGCGTAGCCT
CCAGAGCCGCATCCTC

Alignment

ORF - retro_vpac_456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 56.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VCAASGCDQKFNTKSNLKKHFERKHENQQKQYVCRFEGCEKAFKKHQQLKSHQCQHTRE-PLFRCTHEGC
          .CAAS.C..K..TKSNL.KH...KHENQ.KQYV...EGCE..F.KH.QLK.HQ.Q...E..LFRCT..GC
Retrocopy LCAASLCAHKCHTKSNLRKHLISKHENQPKQYVGSSEGCE-TFQKHLQLKIHQYQQNNE<ALFRCT-QGC

Parental  GKHFSSPSSLK-RHGKVHEGYVCQKECSFVAKTWTELLKHMRETHKEEITCDVCQKTFKRRDYLKQHMKT
          GKH...P.....RH.K..E.YV.Q.ECSF.AKTWT..L...RETHK.E..CD...KTF....YL..HMKT
Retrocopy GKHVTYPXXXPWRHPKIQEDYVFQRECSFAAKTWTKIL-NVRETHKAETICDTSGKTF*LEAYLRRHMKT

Parental  HAPERDV-YRCPREGCGRTYTTVFNLQSHIL
          ..P.RDV..RC..EGCGRT.T....LQS.IL
Retrocopy QVPDRDV<SRCRTEGCGRTATAARSLQSRIL

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_456 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_456 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456 ,