RetrogeneDB ID: retro_vpac_212

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2868:1906462..1906774(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSVPAG00000007009
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_vpac_212
CTGTGTTAGTGTGTTACGATGCTCTCTCCTACCAGCCTGGCTAGTGAGATGACCAGCAGTAAAGTGAAATATTTAAGGCT
CTCCAGCACAGATGATGGCTACAGCGACCTTCAGTTTAAGAAAAGCCCTCCTGAGTTCCCACCTAAAGCCCCGCTGAGCT
TGCTACAATGCTGTTTTTCATTGGTGCTTTGCTCATTAAGACAGGCTCCCTTTGGTTTGTGTGCCCAGCAGCAAAGGGCG
CGCACACCTGCCATTCTAGTCCTGATCACTGGCATTCTGGTGTTCCTGCTGGGCTCTTTCCACTTGTGCATC

Alignment

ORF - retro_vpac_212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 83.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LCQRVMMPSRTNLATGIPSSKVKYSRLSSTDDGYIDLQFKKS-PPKIPYKAIA-LATVLFLIGTFLIIIG
          LC..V.M.S.T.LA....SSKVKY.RLSSTDDGY.DLQFKKS.P...P....A.LAT.LF.IG..LI..G
Retrocopy LC*CVTMLSPTSLASEMTSSKVKYLRLSSTDDGYSDLQFKKS<PS*VPT*SPAELATMLFFIGALLIKTG

Parental  SL-LLAGYISKGGADR-AVPVLIIGILVFLPGFYHLRI
          SL.L.....SKG.A...A..VLI.GILVFL.G..HL.I
Retrocopy SL<LVCVPSSKGRAHL<AILVLITGILVFLLGSFHLCI

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_212 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_212 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Echinops telfairi	ENSETEG00000018264	2 retrocopies	retro_etel_1604, retro_etel_665,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,
Vicugna pacos	ENSVPAG00000007009	1 retrocopy	retro_vpac_212 ,