RetrogeneDB ID: retro_vpac_35

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1078:157134..157518(-)
• Located in intron of: ENSVPAG00000006406

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1B
• Ensembl ID: ENSVPAG00000011892
• Aliases: None
• Description: MOB kinase activator 1B [Source:HGNC Symbol;Acc:29801]

Sequence

>retro_vpac_35
AAGACATTCCGGCCTAAGAGGAAATTTGAACCTGGCACACAGAGGTTCGAACTCCACAAACGAGCTCAAGCATCCCTCAA
CTCGGGTGTGGACCTGAAGGCAGCTGTGCAGCTGCCCAGCGGGGAGGACCAGAACGACTGGGTGGCGGTGCACGTGGTGG
ACTTCTTCAATCGGATCAACCTCATCTACGGGACCATCTGTGAGTTCTGCACCGAGCGGACCTGCCCTGTGATGTCAGGG
GGCCCCAAATATGAGTATCGGTGGCAGGATGACCTCAAGTACAAGAAGCCGACTGCCTTGCCAGCTCCCCAGTACATGAA
CCTTCTCATGGATTGGATCGAGGTCCAGATCAACAACGAGGATATATTTCCAACATGTGTAGGT

Alignment

ORF - retro_vpac_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.91 %
• Parental protein coverage: 68.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTFKPKKNIPEGSHQYELLKHAEATLGSG-NLRMAVMLPEGEDLNEWVAVNTVDFFNQINMLYGTITDFC
          KTF.PK.....G....EL.K.A.A.L.SG..L..AV.LP.GED.N.WVAV..VDFFN.IN..YGTI..FC
Retrocopy KTFRPKRKFEPGTQRFELHKRAQASLNSGVDLKAAVQLPSGEDQNDWVAVHVVDFFNRINLIYGTICEFC

Parental  TEESCPVMSAGPKYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDETLFPSKIG
          TE..CPVMS.GPKYEY.W.D....KKP....AP.Y...LM.W...Q...E..FP...G
Retrocopy TERTCPVMSGGPKYEYRWQDDLKYKKPTALPAPQYMNLLMDWIEVQINNEDIFPTCVG

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_35 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_35 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012418	3 retrocopies	retro_chof_1124, retro_chof_1337, retro_chof_660,
Macropus eugenii	ENSMEUG00000014210	1 retrocopy	retro_meug_384,
Microcebus murinus	ENSMICG00000006469	2 retrocopies	retro_mmur_1622, retro_mmur_653,
Myotis lucifugus	ENSMLUG00000005838	1 retrocopy	retro_mluc_1067,
Ochotona princeps	ENSOPRG00000009133	1 retrocopy	retro_opri_386,
Sus scrofa	ENSSSCG00000008941	2 retrocopies	retro_sscr_377, retro_sscr_586,
Vicugna pacos	ENSVPAG00000011892	1 retrocopy	retro_vpac_35 ,