RetrogeneDB ID: retro_vpac_366

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_12555:6411..7163(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC90B
• Ensembl ID: ENSVPAG00000007753
• Aliases: None
• Description: coiled-coil domain containing 90B [Source:HGNC Symbol;Acc:28108]

Sequence

>retro_vpac_366
TGGAGTCGCCGGGTTTGGCGGCTCCTGGGTTCCGAAGACAGTAGGGGCCGCTGGGCTTCAACTCCCCGCGGGCGTTTCTT
GCCTGTCCTGCGGAGAGACTTCTTCACCACCACAACCAAGGAAGGATATGATATGAGGCAAGTGGACATAACTGCTTTAG
GACAAAGAAAATTAAATTTTGATACCCATGTATTGGTTCAGGACTTGGAAACTCATGGATTTGACAAACACAAGAAGAAA
CAACTGTATCAGCATTAACCATTTTATCAAGTATCAGCTTGGATACTATCTATAAAGGAGATAGCCACTCAAGCTCAATA
GGAAATAACCGTACAACAGCTAATGACTCATTTGGACTCCATCAGGAAAGACATGGTCATCCTAGAGAAAAGTGAATTTG
CAAATCTGAGAGCAGAGAACCAGAAAATGAAAATTGAATTAGAACAAGTTAAGCAATAACTGATAGATGAAACTAGTCGA
ATCAGAGCAGATAATAAACTGGATATCAACCTGGAAAGGAGCAGAGTCACAGATATGATCAAGAAAAGAAACTTATGGAA
GCAACCACAGAATTTATCAGAAAAGATACCACAACCAGAAGTATTATTTCAGGGACTGGTAACACAATTGACACTGAAAT
TGCTTCTTTAAAAATGCTGATGGAGTCTGAGAAGCTTGAGACGATTCGTTATCTTGCAGCCTCAGTGTTTACTTGCCTGG
TAATAGCACAGGGATTTTATAGACTCTGGAAA

Alignment

ORF - retro_vpac_366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.47 %
• Parental protein coverage: 99.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WSRRVWLLLRSEGSGGRRASTPRGRFSLALPRDFFTTTTKEGYDMRQVDITPLGQRKLTFDTHALVQDLE
          WSRRVW.LL.SE.S.GR.ASTPRGRF...L.RDFFTTTTKEGYDMRQVDIT.LGQRKL.FDTH.LVQDLE
Retrocopy WSRRVWRLLGSEDSRGRWASTPRGRFLPVLRRDFFTTTTKEGYDMRQVDITALGQRKLNFDTHVLVQDLE

Parental  AHGFDK-AQAETIVSALTTLSNVSLDTIY-KEMATQAQQEITVQQLIAHLDSIRKDMVILEKSEFANLRA
          .HGFDK..Q.ET.VSALT.LS..SLDTIY.KE.ATQAQ.EITVQQL..HLDSIRKDMVILEKSEFANLRA
Retrocopy THGFDK<TQEETTVSALTILSSISLDTIY>KEIATQAQ*EITVQQLMTHLDSIRKDMVILEKSEFANLRA

Parental  ENQKMKIELEQVKQQLINETSRIRADNKLDINLERSRVTDMFTDQEKKLMEATTEFTRK-DTTTRSIISE
          ENQKMKIELEQVKQ.LI.ETSRIRADNKLDINLERSRVTDM.......L.........K.DTTTRSIIS.
Retrocopy ENQKMKIELEQVKQ*LIDETSRIRADNKLDINLERSRVTDMI--KKRNLWKQPQNLSEK<DTTTRSIISG

Parental  TGNKIDTEIASLKTLMESNKLETIRYLAASVFTCLAIALGFYRLWK
          TGN.IDTEIASLK.LMES.KLETIRYLAASVFTCL.IA.GFYRLWK
Retrocopy TGNTIDTEIASLKMLMESEKLETIRYLAASVFTCLVIAQGFYRLWK

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_366 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_366 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010541	2 retrocopies	retro_chof_1396, retro_chof_780,
Callithrix jacchus	ENSCJAG00000014547	1 retrocopy	retro_cjac_219,
Homo sapiens	ENSG00000137500	1 retrocopy	retro_hsap_3050,
Macaca mulatta	ENSMMUG00000020154	2 retrocopies	retro_mmul_1880, retro_mmul_773,
Nomascus leucogenys	ENSNLEG00000016478	1 retrocopy	retro_nleu_1644,
Ochotona princeps	ENSOPRG00000004144	2 retrocopies	retro_opri_197, retro_opri_682,
Pongo abelii	ENSPPYG00000003736	1 retrocopy	retro_pabe_2525,
Pan troglodytes	ENSPTRG00000004129	1 retrocopy	retro_ptro_1990,
Pteropus vampyrus	ENSPVAG00000005459	1 retrocopy	retro_pvam_614,
Rattus norvegicus	ENSRNOG00000009462	1 retrocopy	retro_rnor_868,
Tupaia belangeri	ENSTBEG00000014665	2 retrocopies	retro_tbel_3436, retro_tbel_4221,
Tarsius syrichta	ENSTSYG00000011196	1 retrocopy	retro_tsyr_710,
Tursiops truncatus	ENSTTRG00000003998	1 retrocopy	retro_ttru_445,
Vicugna pacos	ENSVPAG00000007753	1 retrocopy	retro_vpac_366 ,