RetrogeneDB ID: retro_vpac_308

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_622:455478..455909(-)
• Located in intron of: ENSVPAG00000003994

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC3
• Ensembl ID: ENSVPAG00000003247
• Aliases: None
• Description: ER membrane protein complex subunit 3 [Source:HGNC Symbol;Acc:23999]

Sequence

>retro_vpac_308
GTCCTAATTCAAAGCATAGTCCTCAAGGAAAATGGAAATTATATTCCCAAACAGTCCTTGACATGAAACTATTACTTCAA
CAATCCAGAGGACGGATTTTTCAAAAAAAAAAAAAATAAAGGGAAAACAGTACCACCTTCTGACTGATCCCACTATGCTT
ACAGACACAATGAAAGCGAATGTCACAAAGTCCTCCCTATGATTCTTATTGGTAGATGGATCAACATGACTTTCTCAGGC
TTTGTTACAAAGTCCTATTTCTAATTAATCTATTTTAAGCCTATGCTACAGCAAGGAATTGAACTACTCACAATAGCTGC
ATCTTGGTGAGTTTTACATCCTGGTACTTCTGCTATGTACTTGGGTTTCAGAGCATTTACTCTCTGGTTCTGGGCCAAGG
TAATGCGAATGACCAATCAGGAATGATGCAG

Alignment

ORF - retro_vpac_308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 56.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLIRSRVLRENGKYIPKQSFLTRKYYFNNSEDGFFKKTKRKVVPPSP-MTDPTMLTDMMKGNVTN-VLPM
          VLI.S.VL.ENG.YIPKQS.LT..YYFNN.EDGFF.....K.....P..TDPTMLTD.MK.NVT..VLPM
Retrocopy VLIQSIVLKENGNYIPKQS-LT*NYYFNNPEDGFFXXXXXKGKTVPP>LTDPTMLTDTMKANVTK<VLPM

Parental  ILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLTLDASW-VSSASWYFLNVFGLRSIYSLILGQD
          ILIG.WINMTFSGFVT.K..F.L...FKPMLQQGIELLT..ASW.VS..SWYF..V.G..SIYSL.LGQ.
Retrocopy ILIGRWINMTFSGFVT-KSYF*L-IYFKPMLQQGIELLTIAASW<VSFTSWYFCYVLGFQSIYSLVLGQG

Parental  NAADQSRMMQ
          NA.DQS.MMQ
Retrocopy NANDQSGMMQ

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_308 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_308 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005202	1 retrocopy	retro_cfam_730,
Callithrix jacchus	ENSCJAG00000037305	1 retrocopy	retro_cjac_3209,
Equus caballus	ENSECAG00000024410	1 retrocopy	retro_ecab_737,
Felis catus	ENSFCAG00000024898	2 retrocopies	retro_fcat_1932, retro_fcat_2002,
Microcebus murinus	ENSMICG00000002333	2 retrocopies	retro_mmur_439, retro_mmur_707,
Mustela putorius furo	ENSMPUG00000017149	1 retrocopy	retro_mputfur_456,
Pteropus vampyrus	ENSPVAG00000012615	3 retrocopies	retro_pvam_1260, retro_pvam_1278, retro_pvam_1439,
Tursiops truncatus	ENSTTRG00000007554	2 retrocopies	retro_ttru_1311, retro_ttru_285,
Vicugna pacos	ENSVPAG00000003247	2 retrocopies	retro_vpac_308 , retro_vpac_461,