RetrogeneDB ID: retro_vpac_403

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_1604:25764..26336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSVPAG00000011814
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_vpac_403
GGTTATGGAGGTTTTGATGACTATGGTGGCTATAATAACTCTGGCTATGGAAATGATGGCTTTGATGACAGATTGCAAGA
TGTAAGAGGTATGAGAGGTCACAGCTATGGTGGAGCCGCTGATGCAAGTTCAGGTTTTCATGGTGGTCATTTTGTACATA
TGAGAGGATCATGTTTTCTTTCAAGTGAAAATGACATTGCTAATTTCTTCTCACCACTAAATCCAATACTAGTTCATAGT
GATATTGAAGCTGAAGGCAGAGCAACAAGAGAAGCAGATGTAGAGTTTATGACATGTGAAGATGCAGTAGCTTGCCACGT
CTGAAGATAAGAATAACATGCAACATCAATACATTGAACTCCTCTTGAATTCTAGTCCTGGAGATGGTTCTGGAACGGGA
AGTTCTAGAATGGAATGTTACAGAAAAGATGGAGCAAATGAAAAGAGAGATTATGAATCTGTTGGAAGAATGGGAATGGG
AAACCATTTACAGTGGTATTCCTGATGGCTTAGGTGGTGGTGGGGTCGGTGGAGGTTACCACGGACAAGACGGCATGAAT
GGAGGTGGATGG

Alignment

ORF - retro_vpac_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.36 %
• Parental protein coverage: 56.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GYGGFDDYGGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFF
          GYGGFDDYGGYNN.GYGNDGFDDR..D.RGM.GH.YGGA.DASSGFHGGHFVHMRG..F...ENDIANFF
Retrocopy GYGGFDDYGGYNNSGYGNDGFDDRLQDVRGMRGHSYGGAADASSGFHGGHFVHMRGSCFLSSENDIANFF

Parental  SPLNPIRVHIDIGADGRATGEADVEFVTHEDAVA-AMSKDKNNMQHRYIELFLNSTPGGGSGMGGSGMGG
          SPLNPI.VH.DI.A.GRAT.EADVEF.T.EDAVA.A.S.DKNNMQH.YIEL.LNS.PG.GSG.G.S.M..
Retrocopy SPLNPILVHSDIEAEGRATREADVEFMTCEDAVA>ATSEDKNNMQHQYIELLLNSSPGDGSGTGSSRMEC

Parental  YGRDGMDNQGGYGSVGRMGMGNN-YSGGYGTPDGLGGYGRGGGGSGGYYGQGGMSGGGW
          Y..DG......Y.SVGRMGMGN..YSG....PDGLGG.G.GGG....Y.GQ.GM.GGGW
Retrocopy YRKDGANEKRDYESVGRMGMGNH>YSG---IPDGLGGGGVGGG----YHGQDGMNGGGW

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_403 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_403 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403 ,