RetrogeneDB ID: retro_vpac_599

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_6399:26778..27188(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAUS2
• Ensembl ID: ENSVPAG00000006260
• Aliases: None
• Description: HAUS augmin-like complex, subunit 2 [Source:HGNC Symbol;Acc:25530]

Sequence

>retro_vpac_599
ATGGCTGTGGCAAACCCCTGGGACAAGGTGTCCATGCTTAATGCCGCCAGGCTACTGCTGGGCCATTTTGTGGTTTCAGG
GTTGATCACTCAGGAGATGTTAAACATATCTAAGAAATTAGCTTCCCGTTTTGTGAACTTCTCCAGACCACAGCAGATCA
CAGATAACCAAGCTGAAATCTACCAGAAAAACTCTGAACTCCTTAGACTAGAAAAAGATACAGCAGATATTGTCCATCCT
TCCTTTTTGGCTCAAAAGTGTCATACTCTGCAAAGCACGAATAATCATTCAGAAGCAGTGCCCGAAGAGAAGCGGTCCCT
CAGCAAAGACTATTGAAACCCGTGTGCCAAGAAAACTTGCCTATTGAAGTTATTTATCACAGATACATGGTATATTTGTT
GGAGTTGGCA

Alignment

ORF - retro_vpac_599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 59.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAENPWDPASAPNAAGLLLGHFVASGVVTQDMLNISKKSDSCFVNFSRLQQITDIQAEIYQKNLEIELL
          MA..NPWD..S..NAA.LLLGHFV.SG..TQ.MLNISKK..S.FVNFSR.QQITD.QAEIYQKN...ELL
Retrocopy MAVANPWDKVSMLNAARLLLGHFVVSGLITQEMLNISKKLASRFVNFSRPQQITDNQAEIYQKN--SELL

Parental  RLEKDTADVVHPSFLAQKCHTLQSMNNHLEAVLKEKRSL-RQRLLKPMCQENLPIEAVYHRYMVHLLELA
          RLEKDTAD.VHPSFLAQKCHTLQS.NNH.EAV..EKRSL..QRLLKP.CQENLPIE..YHRYMV.LLELA
Retrocopy RLEKDTADIVHPSFLAQKCHTLQSTNNHSEAVPEEKRSL<QQRLLKPVCQENLPIEVIYHRYMVYLLELA

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_599 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_599 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003587	4 retrocopies	retro_meug_1171, retro_meug_1231, retro_meug_702, retro_meug_996,
Microcebus murinus	ENSMICG00000000819	1 retrocopy	retro_mmur_648,
Monodelphis domestica	ENSMODG00000017882	1 retrocopy	retro_mdom_1473,
Oryctolagus cuniculus	ENSOCUG00000011004	1 retrocopy	retro_ocun_1322,
Sorex araneus	ENSSARG00000001275	2 retrocopies	retro_sara_123, retro_sara_413,
Ictidomys tridecemlineatus	ENSSTOG00000006207	1 retrocopy	retro_itri_618,
Vicugna pacos	ENSVPAG00000006260	1 retrocopy	retro_vpac_599 ,