RetrogeneDB ID: retro_vpac_498

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_254090:2..489(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TTC1
• Ensembl ID: ENSVPAG00000012031
• Aliases: None
• Description: tetratricopeptide repeat domain 1 [Source:HGNC Symbol;Acc:12391]

Sequence

>retro_vpac_498
ATGGAGGAGAAGTCAGAAAACTGTAGGGTTCCAGAGGATCTGTTTAATGGTTTGAAAATTACAGATCCCCCAGGAAGCGG
AGGGTGCTAGTCCGCCAGTTTCTAATGCCAAAGATCACCATTCCCAGAGCAAACTGCTCCAGGTTGTTGAGACCCATCCC
CAGGAGGACCAGGTAAAAGAGGAGAGCTTTTATGACCCCAGTGCCTCATTTGAGAAGGAGAAACCAAGAGTGGATGAGGT
TGAAAACAAACCTGAAAATGATGGGAATTCCTTTGAACTAGATGAAGAATATCCAATAGAACTGGAAAGAAACATGCCCG
ATGAAGAGAAAAAGAAAAGGAGAGAAGAGAGCACTAGACTAAAGGAGGAGGGAAATGAGCAGTTTAAGAAAGGAGGTTAT
GTGGAAGCTGAAAGTTCTTACAGGCGAACCCTTCAGATGTGTCTGTCCTGCTTCCAGAAAGACGGGTCTATTTTGTTTTC
AAACAGA

Alignment

ORF - retro_vpac_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.34 %
• Parental protein coverage: 65.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEKSKNCRVPEDLFNGLKVTDP-QEAEGASPPVSNAKDHHSQSKLLQDVETHPQEDQGEEECFYDPSAS
          MEEKS.NCRVPEDLFNGLK.TDP.QEAEGASPPVSNAKDHHSQSKLLQ.VETHPQEDQ..EE.FYDPSAS
Retrocopy MEEKSENCRVPEDLFNGLKITDP>QEAEGASPPVSNAKDHHSQSKLLQVVETHPQEDQVKEESFYDPSAS

Parental  FEKEEPRVDEVENKPENDVNSSELDEEYLVELEKNMPDEEKKKRREESTRLKEEGNEQFKKGDYMEAESS
          FEKE.PRVDEVENKPEND.NS.ELDEEY..ELE.NMPDEEKKKRREESTRLKEEGNEQFKKG.Y.EAESS
Retrocopy FEKEKPRVDEVENKPENDGNSFELDEEYPIELERNMPDEEKKKRREESTRLKEEGNEQFKKGGYVEAESS

Parental  YSRALQMCPSCFQKDRSILFSNR
          Y.R.LQMC.SCFQKD.SILFSNR
Retrocopy YRRTLQMCLSCFQKDGSILFSNR

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_498 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_498 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019397	1 retrocopy	retro_etel_1659,
Myotis lucifugus	ENSMLUG00000003057	2 retrocopies	retro_mluc_1351, retro_mluc_2408,
Otolemur garnettii	ENSOGAG00000016342	1 retrocopy	retro_ogar_1052,
Tupaia belangeri	ENSTBEG00000004641	1 retrocopy	retro_tbel_3250,
Vicugna pacos	ENSVPAG00000012031	1 retrocopy	retro_vpac_498 ,