RetrogeneDB ID: retro_vpac_447

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_20202:1696..2564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX4
• Ensembl ID: ENSVPAG00000002377
• Aliases: None
• Description: thioredoxin-related transmembrane protein 4 [Source:HGNC Symbol;Acc:25237]

Sequence

>retro_vpac_447
TACGCCCCGTGGTGTCTATCTTGTCAGCAGACTGATTCAGAATGGGAGACATTTGCAAAGAATGGTGAAATACTTCAGAT
CAGTGTGGGGAAGGTAGATGTCATTCAAGAACCAGGTTTGAGTGGCCGCTTCTTTGTCACCACCCTCCCAGGATTTTTTC
ATGCGAAGGATGGGGTATTCCGCTGTTACTGTGGCCCAGGAGTCTAGGAAGACCTTCAGAATTATATCTTAGAGAAGAAA
CGGCAATCAGTTGAGCCTCTGCCTGGCTGGAAATCCCTGGCTTCTCTAACGATGTCTGGAATGGCTGGTCTTTTTAGTAT
CTCTGGCAAGATACGGCATCTTCACAACTATTTCACAGTGACCCTTGGAGTACCTGCTTGGAGTTCTTATGTCTTTTTAG
TTGTAGCCACCTTGATTTTTGGCCTTCTCATGGGTCTGGTCTTGGTGGTAGTATCAGAATGCTTCTCTATGCCACTTCCA
CGACATTTATCTGAACATTCTGAGCAGAATCTGAGGTCAGAGGAGGCTCATGCGGCTGCAGTTGCAGGATGCAGAGGAGG
AAAAGAGGAGGAATTCAAATGAGAAGAAAACCAAGGACCGCCTTGTAGATGAGGAGTAAGAGAAAGAAGAGCTGGGTGAT
GACGAAGCAGAGGAGGAAGAGGAGGACGGCCCGGCCGCTGGTGCAGACGAGGAGAGGGGTGCCGCCCAGGACGCGGCCCT
GAGAGAGGCCTGGGAGGACGTCGGGCCAGAGGTCGGGCCGGGCGAGGCTCTGGACGCTGCCTCCGAGCAGCGCCCTTCAG
CCGACGCAGAGGTGGCAGAAGACACTCTGAGGCAGCGTAGAAGTCAGCATGCTGACAAGGGGCCGTCG

Alignment

ORF - retro_vpac_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAPWCPSCQQTDSEWEMFAKNGEILQISVGKVDVIQEPGLSGRFFVTTLPAFFHAKDGIFRRYRGPGVYE
          YAPWC.SCQQTDSEWE.FAKNGEILQISVGKVDVIQEPGLSGRFFVTTLP.FFHAKDG.FR.Y.GPGV.E
Retrocopy YAPWCLSCQQTDSEWETFAKNGEILQISVGKVDVIQEPGLSGRFFVTTLPGFFHAKDGVFRCYCGPGV*E

Parental  DLQNYILEKKWQSVEPLTGWKSPSSLTXXXXXXXXXXXXXXXHLHNYFTVTLGVPAWCSYVFFVVATLIF
          DLQNYILEKK.QSVEPL.GWKS..SLT...............HLHNYFTVTLGVPAW.SYVF.VVATLIF
Retrocopy DLQNYILEKKRQSVEPLPGWKSLASLTMSGMAGLFSISGKIRHLHNYFTVTLGVPAWSSYVFLVVATLIF

Parental  GLLMGLVLVVISECFSMPLPRHLSEHSGQTLRSEEAHAA-EQLQDAEEEKEDSNEEENKDSLVDEEEEKE
          GLLMGLVLVV.SECFSMPLPRHLSEHS.Q.LRSEEAHAA.......EE....SNE...KD.LVDEE.EKE
Retrocopy GLLMGLVLVVVSECFSMPLPRHLSEHSEQNLRSEEAHAA>QLQDAEEEKRRNSNEKKTKDRLVDEE*EKE

Parental  ELGDEDEAEEEEEDGPAAGADEERSAAQDPAPREAGRTWADVGPD----EALDAASEQPPSTDAEVAEDT
          ELGD.DEAEEEEEDGPAAGADEER.AAQD.A.REA...W.DVGP.....EALDAASEQ.PS.DAEVAEDT
Retrocopy ELGD-DEAEEEEEDGPAAGADEERGAAQDAALREA---WEDVGPEVGPGEALDAASEQRPSADAEVAEDT

Parental  LRQRRSQHADKGPS
          LRQRRSQHADKGPS
Retrocopy LRQRRSQHADKGPS

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_447 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_447 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Vicugna pacos	ENSVPAG00000002377	1 retrocopy	retro_vpac_447 ,