RetrogeneDB ID: retro_vpac_380

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_142048:759..1330(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000004599
• Aliases: None
• Description: None

Sequence

>retro_vpac_380
GAGAGAGCGTGCGACCTGGTCTTCACCAAGATGAGGGGCGGCCGCCCTGGCCGCCCAGATTGATGAACTCCCAGAGGGAG
CTGTGAGGCCTCCGGCAAATAAGTATCCTCTTACTTTTTTGGCACCCATGAAACTCCATTTTTAGATCCCAAAGACCTTT
TCCCTTATAAGAAAAACAAAGGCAAGTTTGGAAAGTCAAACAAATGGAAAGGGCTTAATGAGGGGTTATGGGAAATAGAA
AATAGCCCAGGAGTAGAGTTTCCTGCACACCAGGCAGTTCAGCACCAAAGCTCCTCAGAAACTGAGGAGAAGGCGGGATC
CTGCAGATGCAGGCCTTGAGGAAGAAGGTGATAGAGTAGAAGAAGATGGACAAGGCAAAAGAAAGAGTGAAAAACCAGGG
TCAAAACAGAAGAAGTCATATACTTCAAAGAAATTCTCTAAACAATCCTGGAAATATCCAGCATATGAAGATGACAAGGA
CTGCAAAGAAGAAAATAAAAGCAGCTCTGAGGGTGGAGATGCTGGCAATGACACAATAAACACTTTAGACTTGCAGAAAA
CCAGTGAAGGG

Alignment

ORF - retro_vpac_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.66 %
• Parental protein coverage: 95.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEACDLVFTKMRGG-PWPPKIDELPEGAVKPPANKYPI-FFFGTHETAFLGPKDLFPYKEYKDKFGKSNK
          E.ACDLVFTKMRGG......IDELPEGAV.PPANKYP...FFGTHET.FL.PKDLFPYK..K.KFGKSNK
Retrocopy ERACDLVFTKMRGG>ALAAQIDELPEGAVRPPANKYPL<YFFGTHETPFLDPKDLFPYKKNKGKFGKSNK

Parental  RKGFNEGLWEIENNPGVKFTGYQAIQQQSSSETE-GEGG-NTADASSEEEGDRVEEDGKGKRKNEKAGSK
          .KG.NEGLWEIEN.PGV.F...QA.Q.QSSSETE.GEGG...ADA..EEEGDRVEEDG.GKRK.EK.GSK
Retrocopy WKGLNEGLWEIENSPGVEFPAHQAVQHQSSSETE<GEGG<DPADAGLEEEGDRVEEDGQGKRKSEKPGSK

Parental  RKKSYTSKKSSKQSRKSPGDEDDKDCKEEENKSSSEGGDAGNDTRNTTSDLQKTSEG
          .KKSYTSKK.SKQS.K.P..EDDKDCK.EENKSSSEGGDAGNDT.NT..DLQKTSEG
Retrocopy QKKSYTSKKFSKQSWKYPAYEDDKDCK-EENKSSSEGGDAGNDTINTL-DLQKTSEG

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_380 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_380 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380 ,