RetrogeneDB ID: retro_vpac_509

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_271876:192..765(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000011474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DTWD1
• Ensembl ID: ENSVPAG00000008358
• Aliases: None
• Description: DTW domain containing 1 [Source:HGNC Symbol;Acc:30926]

Sequence

>retro_vpac_509
CACCTGAGTTTGTAAGTTTATAGGTTTTAAGGTATTTATACATGTCCTTGTATTCCAGACTATGAAGAAAAGGACCATGA
AGTTGCACCTATTTTTCCTGAACCTATGTCTGTCTCAATAAAAGGTATTTCTTTTCATTTGCAAAAAAGGATTCAAAATA
ATGTAGAGGCAAAGATGATGGCCCTGACAAGCTACCCATTAAATGCAAGAAAACTGAAGAAACAGGATTTGAATGACATT
AAGTGCAAAGACAAAACACTGAAAAAAAATTTATTTACAGATAGCACCTGGAACCAAACAAACAAAAATATTCACTAATG
AGAGATTTCAAGGGTTGCTAGGAGTTGAAAACAAGAAAAACTTGCTTTTGGAGCCATCAGAAGGGAAAGCCAGATACTTT
CCTTTCCACAATGGGAGCCATTTACTACTTTTTGGTAGACAACCGTACTGATTTATTAAAAGAGAAATACAAAGGACAAC
TTGATAACCTTCTAGTTTTCCTACTTTTTTATGTACCAGTTGATAAAGAACGCCAAATGCCCTGGAGACAAGGAAACAAG
AAAGCTTAACCGT

Alignment

ORF - retro_vpac_509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.51 %
• Parental protein coverage: 63.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HAKLLAPEFVNIYTYPCIPEYEEKDHEVALVFPGPKSVSVKDISFHLQKRIQN-VRSK-NDDPDKPSIKR
          H..L....F..IYT.PCIP.YEEKDHEVA..FP.P.SVS.K.ISFHLQKRIQN.V..K..D.PDK..IK.
Retrocopy HLSL*VYRF*GIYTCPCIPDYEEKDHEVAPIFPEPMSVSIKGISFHLQKRIQNNVEAK<DDGPDKLPIKC

Parental  KKTEEQG-LNDSKCEDTTLKKIVFIDSTWNQTN-KIFTDERLQGLLQVELKTRKTCFWRHQKGK-PDTFL
          KKTEE.G.LND.KC.D.TL....F.DSTWNQTN.KIFT.ER.QGLL.VE....K........GK.PDTFL
Retrocopy KKTEETG>LNDIKCKDKTLXXXLFTDSTWNQTN>KIFTNERFQGLLGVE--NKKNLLLEPSEGK>PDTFL

Parental  STIEAIYYFLVDYHTDILKEKYKGQYDNLLFF-YSFMHQLIKNAKCPGNKETRKLTR
          ST..AIYYFLVD..TD.LKEKYKGQ.DNLL.F.Y.FM.QLIKNAKCPG.KETRKL.R
Retrocopy STMGAIYYFLVDNRTDLLKEKYKGQLDNLLVF>YFFMYQLIKNAKCPGDKETRKLNR

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_509 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_509 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014926	1 retrocopy	retro_cfam_2081,
Cavia porcellus	ENSCPOG00000003461	2 retrocopies	retro_cpor_1476, retro_cpor_250,
Homo sapiens	ENSG00000104047	1 retrocopy	retro_hsap_2846,
Gorilla gorilla	ENSGGOG00000027921	1 retrocopy	retro_ggor_1973,
Nomascus leucogenys	ENSNLEG00000006167	1 retrocopy	retro_nleu_1598,
Otolemur garnettii	ENSOGAG00000013291	1 retrocopy	retro_ogar_499,
Ochotona princeps	ENSOPRG00000002951	2 retrocopies	retro_opri_136, retro_opri_949,
Pongo abelii	ENSPPYG00000006464	2 retrocopies	retro_pabe_2355, retro_pabe_2356,
Pan troglodytes	ENSPTRG00000007058	1 retrocopy	retro_ptro_1928,
Vicugna pacos	ENSVPAG00000008358	2 retrocopies	retro_vpac_509 , retro_vpac_530,