RetrogeneDB ID: retro_vpac_283

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3642:1881346..1881664(-)
• Located in intron of: ENSVPAG00000003780

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSVPAG00000000931
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_vpac_283
ATAAGGGGGCGACAAGACTTTGCTTTATTTTATTCCATCATATCACAGTCCACATTCAATGATTTACAAGATCTGGGAAA
ACAGAGAACAACAGTTAAGGACTGTTCTAGATGTTCTAGAGATTCTGGTTGGTGATAAGTGTGACTTGGAACATGACAGA
GTGGTAGGAAAGGAACAAGGTCAAAATGTAGCAAGACAGTGGAACAATTGTGCATTCTTAGAATCCTCTGCAAAATAGAA
AATAAGTATTAATGAATCTCTTGTGACCCAGAGTGGCAAATTAACAGAAAAACTCCACTCTCTGGGAAGACCCGCAAA

Alignment

ORF - retro_vpac_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.52 %
• Parental protein coverage: 57.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTD-DVPMILVGNKCDLEDERVVGKEQGQNLARQWNN
          ....Q.FAL.YSI..QSTFNDLQDL..Q...VKD...DV..ILVG.KCDLE..RVVGKEQGQN.ARQWNN
Retrocopy IRGRQDFALFYSIISQSTFNDLQDLGKQRTTVKDCS>DVLEILVGDKCDLEHDRVVGKEQGQNVARQWNN

Parental  CAFLESSAKSKINVNE-IFYDLVRQINRKTPVPGKARK
          CAFLESSAK.KI..NE.I..D...QINRKTP..GK.RK
Retrocopy CAFLESSAK*KISINE<ISCDPEWQINRKTPLSGKTRK

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_283 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_283 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 17 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Myotis lucifugus	ENSMLUG00000016606	2 retrocopies	retro_mluc_1126, retro_mluc_2211,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Procavia capensis	ENSPCAG00000010977	1 retrocopy	retro_pcap_8,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tursiops truncatus	ENSTTRG00000015712	2 retrocopies	retro_ttru_1105, retro_ttru_134,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283 , retro_vpac_408,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,