RetrogeneDB ID: retro_vpac_139

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_2055:599976..600355(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSVPAG00000011472
• Aliases: None
• Description: density-regulated protein [Source:HGNC Symbol;Acc:2769]

Sequence

>retro_vpac_139
AATTCACCCAAACAAGAAGCTGGAATTAGTGAGGGTCAAGGAACAGCAGGGGAAGAGGAAAAGAAGAGAAAACAAAAGAG
AAGTGGGAGGGGTCAAATAAAACAAAAACAGAAGACTGTACCCCAAAAGGTTATGACAGCCAAAATTCCCAGAGCAAAGA
AGAAATATGTAACATGAATGTGTGGCCTTGCAACTTTTGAAACTGATCTTAAAGAAGCACAAAGGTTTTTGCTCAGAAAT
TCTCCTGTGGTGCCTCAGTAGCAGGGGAGGATGAAATCATCATTAGGGAGACTTTACAGATGACATAATTGATGCCATTC
AGGTAAAACGGCCAGAGGTGGATGATGATAGCATCGAAGACTTTGGAGAAGTGAAGAAG

Alignment

ORF - retro_vpac_139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 65.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSPKQETGISEGQGTAVAEEEKKKQKRGGRGQIKQKKKTVPQKVTIAKIPRAKKKYVTRVCGLATFEIDL
          NSPKQE.GISEGQGTA..EE.K.KQKR.GRGQIKQK.KTVPQKV..AKIPRAKKKYVT..CGLATFE.DL
Retrocopy NSPKQEAGISEGQGTAGEEEKKRKQKRSGRGQIKQKQKTVPQKVMTAKIPRAKKKYVT*MCGLATFETDL

Parental  KEAQRF-FAQKFSCGASVTGEDEIIIQ-GDFTDDIIDVIQEKWPEVDDDSIEDLGEVKK
          KEAQRF.FAQKFSCGASV.GEDEIII..GDFTDDIID.IQ.K.PEVDDDSIED.GEVKK
Retrocopy KEAQRF<FAQKFSCGASVAGEDEIIIR<GDFTDDIIDAIQVKRPEVDDDSIEDFGEVKK

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_139 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_139 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016012	1 retrocopy	retro_acar_71,
Bos taurus	ENSBTAG00000032433	1 retrocopy	retro_btau_110,
Callithrix jacchus	ENSCJAG00000020488	4 retrocopies	retro_cjac_1665, retro_cjac_2303, retro_cjac_2377, retro_cjac_2627,
Echinops telfairi	ENSETEG00000013029	1 retrocopy	retro_etel_1127,
Myotis lucifugus	ENSMLUG00000002088	1 retrocopy	retro_mluc_2450,
Oryctolagus cuniculus	ENSOCUG00000008150	2 retrocopies	retro_ocun_1325, retro_ocun_1524,
Sorex araneus	ENSSARG00000004446	4 retrocopies	retro_sara_118, retro_sara_125, retro_sara_523, retro_sara_722,
Sus scrofa	ENSSSCG00000009788	1 retrocopy	retro_sscr_1145,
Tursiops truncatus	ENSTTRG00000015856	1 retrocopy	retro_ttru_745,
Vicugna pacos	ENSVPAG00000011472	1 retrocopy	retro_vpac_139 ,