RetrogeneDB ID: retro_vpac_62

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_138:404731..405156(-)
• Located in intron of: ENSVPAG00000011555

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPRD1A
• Ensembl ID: ENSVPAG00000001641
• Aliases: None
• Description: regulation of nuclear pre-mRNA domain containing 1A [Source:HGNC Symbol;Acc:25560]

Sequence

>retro_vpac_62
TTACAAGATCTAGAAAATGCAGCTTCAGGTGTGCAGCATTTCATCAAAGGATAGCTTCTTTGCCTGTTGAAGTTCAAGTA
TCCCTATTAGATAAAATAACAGATAAAGAATCTAGAGAAAGGCTTTCTAAAATGGTAGAGGATGCTTGTGTGTTGCTGGC
AGATTACAATGGCAGACTGGTGGCTGAAATAGATGATTGGAAGCAACTTACTTGAAAGTGAGCAGATTTTCTTGGTTGTC
AAAAGGAAGCCCTTGCAGAGAAAGAGCACAAATTGGAAGAATACAAGTGCAAGTAATCCAGAGATTCCCTGGTGTGCGAA
GAACTCAGGTCCCACATCCAGAGCCTGCCAGACTTATCTCGATTGCCCAATGTCACTGACAGCCACATGCATCTGCCCTT
TGCTGGAGACATCTGCAGTGAAGAT

Alignment

ORF - retro_vpac_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.72 %
• Parental protein coverage: 65.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQDLENAASGD-AAVHQRIASLPVEVQEVSLLDKITDKESGERLSKTVEDACMLLADYNGRLAAEIDDRK
          LQDLENAASG..AA.HQRIASLPVEVQ.VSLLDKITDKES.ERLSK.VEDAC.LLADYNGRL.AEIDD.K
Retrocopy LQDLENAASGV<AAFHQRIASLPVEVQ-VSLLDKITDKESRERLSKMVEDACVLLADYNGRLVAEIDDWK

Parental  QLTRMLADFLRCQKEALAEKEHKLEEYKRKLARVSLVRKELRSRIQSLPDLSRLPNVTGSHMHLPFAGDI
          QLT...ADFL.CQKEALAEKEHKLEEYK.K..R.SLV..ELRS.IQSLPDLSRLPNVT.SHMHLPFAGDI
Retrocopy QLT*K*ADFLGCQKEALAEKEHKLEEYKCK*SRDSLVCEELRSHIQSLPDLSRLPNVTDSHMHLPFAGDI

Parental  YSED
          .SED
Retrocopy CSED

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_62 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_62 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007025	1 retrocopy	retro_eeur_245,
Gorilla gorilla	ENSGGOG00000007369	1 retrocopy	retro_ggor_1237,
Macaca mulatta	ENSMMUG00000018777	1 retrocopy	retro_mmul_1562,
Monodelphis domestica	ENSMODG00000000399	1 retrocopy	retro_mdom_360,
Nomascus leucogenys	ENSNLEG00000006228	1 retrocopy	retro_nleu_1323,
Pongo abelii	ENSPPYG00000009111	1 retrocopy	retro_pabe_1352,
Pan troglodytes	ENSPTRG00000009974	1 retrocopy	retro_ptro_1106,
Vicugna pacos	ENSVPAG00000001641	1 retrocopy	retro_vpac_62 ,