RetrogeneDB ID: retro_vpac_27

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1027:127009..127700(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSVPAG00000007888
• Aliases: None
• Description: annexin A2 [Source:HGNC Symbol;Acc:537]

Sequence

>retro_vpac_27
TCTTTCAAAATGTCTACTGTTCACGAAATTCTGTACAAGCTCAGCTTGGAGGGTGACCACTCCACACCCACAAGTGTGTA
CGGGTCAGTCAAAGCATACACCAACTTTGACGCTGAGTGGGATGCTCTGAACATCGAAATGGCCATCAAGACCAAAGGTG
TGGATGAGGTCACCACTGTCAACATTTTGACCAACTGCAGCAATGAATAGAGACAGGATATTGCCTTTGCCTACCAGAGA
AGTACCAAAAAGAAACTTGCGTCAGCGCTGAAGTCAGACTTGTTCGGCCACCTGGAGACAGTGATTTTGGGCCTGTTGAA
AACACCTGCTCAGTATGACGCTTCAGAGCTGAAAAGCCTCCGTGAAGGGGCTGGGGACTGATGAGGACTCCCTCATTGAG
ATCATCTGCTCAAGGACCAACCAGGAGCTGCAGGAAATTAACAGAGTCTACAAGGAAATGTATAAGACTGAGCTGGAGAG
GGACATCATTTCCGACACACTTGGTGACTTCTGCAAGCTGACGGTTGCCCTTGCCAAGGGTAGATGAGCAGAGGATGGCT
CTGTCGTCGATTACGATCTGATTGACCAAGATGCCCAGGACCTCTACGATGTTGGCTTGAAGAGAAAAGGAACTGATATT
CCCAAGTGGATCAGCATCATGACTGAGCAGAGCGTGTGCCACCTCCAGAAA

Alignment

ORF - retro_vpac_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFKMSTVHEILCKLSLEGDHSTPASAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQ
          SFKMSTVHEIL.KLSLEGDHSTP.S.YGSVKAYTNFDAE.DALNIE.AIKTKGVDEVT.VNILTN.SNE.
Retrocopy SFKMSTVHEILYKLSLEGDHSTPTSVYGSVKAYTNFDAEWDALNIEMAIKTKGVDEVTTVNILTNCSNE*

Parental  RQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELK-ASMKGLGTDEDSLIEIICSRT
          RQDIAFAYQR.TKK.LASALKS.L.GHLETVILGLLKTPAQYDASELK.AS.KGLGTDEDSLIEIICSRT
Retrocopy RQDIAFAYQRSTKKKLASALKSDLFGHLETVILGLLKTPAQYDASELK>ASVKGLGTDEDSLIEIICSRT

Parental  NQELQEINRVYKEMYKTELEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRK
          NQELQEINRVYKEMYKTELE.DIISDT.GDF.KL.VALAKGR.AEDGSV.DY.LIDQDA.DLYD.G.KRK
Retrocopy NQELQEINRVYKEMYKTELERDIISDTLGDFCKLTVALAKGR*AEDGSVVDYDLIDQDAQDLYDVGLKRK

Parental  RSDVPKKITIMTDRSVCNLRK
          ..D.PK.I.IMT..SVC.L.K
Retrocopy GTDIPKWISIMTEQSVCHLQK

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_27 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_27 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 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Myotis lucifugus	ENSMLUG00000002464	3 retrocopies	retro_mluc_1569, retro_mluc_2223, retro_mluc_2431,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Otolemur garnettii	ENSOGAG00000009952	1 retrocopy	retro_ogar_3510,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Tupaia belangeri	ENSTBEG00000001276	1 retrocopy	retro_tbel_3335,
Tarsius syrichta	ENSTSYG00000003719	1 retrocopy	retro_tsyr_2086,
Vicugna pacos	ENSVPAG00000007888	2 retrocopies	retro_vpac_241, retro_vpac_27 ,