RetrogeneDB ID: retro_vpac_630

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_8563:14695..15301(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A16
• Ensembl ID: ENSVPAG00000011819
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; Graves disease autoantigen), member 16 [Source:HGNC Symbol;Acc:10986]

Sequence

>retro_vpac_630
GCCCTGGCGGCAGCTAACCCACCTCCATCTCGAGATGCCGCAGGCAGCAGGAGTCTGAGGGCCCACCGCAGGCAGAGACT
TCTCCTGGCTGTGCTCCTTCCTGGACAGAGGTATTGCTGGATTCTGTGCCAAAACAGTTGCTCTTTTGGATTGAGCAAAG
GTTTTATTACAAGCTCACAATCACCATTACAAACATTTGGGAATATTTCCTGCATTATGTGCTGTTCCCCCAAGGAGGAA
TACCTTGGGTTGTAGAAAGAGAATGTTGCAATGATGATCCAATCTTTCCCTATGGTGCATCCAGTTTATAGCATTTGAGC
ATTGTAGAACAAAAATAACTACGAAGCTGGGAATTTCTGGTCTGTGCACAGATTAATGGCTGGATCCACGGTACATTTAA
ACAGCAGTTCTCTGTACTTACCATTTTCACATGGTTAGAGTGTGCCTAATGTTCCAGGTGAAAGGGGGACATACTTAAAC
AGGAATCATTCATGCATTCAGAACAATTTATGCACAGGAAGGTGGTCTCTTTGCATTTTACAGAGGCCTGATGCTGCTCT
AGTGGGAATGGCTCTCCATCGAGTTGTCTCGTTTTATACTGTTGGG

Alignment

ORF - retro_vpac_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.25 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ALAAAE-PPPA-MPQAAGAGGPAARRDFYWLRSFVAGGIAGCCAKTTVAPLDRVKVLLQAHNHHYKHLGV
          ALAAA..PP...MPQAAG..GP.A.RDF.WL.SF...GIAG.CAKT.VA.LD..KVLLQAHNHHYKHLG.
Retrocopy ALAAANPPPSR>MPQAAGV*GPTAGRDFSWLCSFLDRGIAGFCAKT-VALLD*AKVLLQAHNHHYKHLGI

Parental  FSALRAVP-QKEGYLGLYKGNGAMMIR-IFPYGA-IQFMAFEHYKTLITTKLGISG-HVHRLMAGSMAGM
          F.AL.AVP..KE.YLGL.K.N.AMMI..IFPYGA.IQF.AFEH..T.ITTKLGISG..VHRLMAGS....
Retrocopy FPALCAVP<PKEEYLGL*KENVAMMIQ<IFPYGA<IQFIAFEHCRTKITTKLGISG<SVHRLMAGSTVHL

Parental  -TAVICTYPLDMVRVRLAFQVKGEHTYKGIIHAFTTIYAKEGGFLGFYRGLM-PTILGMAPYAGVSFFTF
          .TAV.CTY...MVRV.L.FQVKG.HT..GIIHAF.TIYA.EGG...FYRGLM.....GMA....VSF.T.
Retrocopy >TAVLCTYHFHMVRVCLMFQVKGGHT*TGIIHAFRTIYAQEGGLFAFYRGLM<AALVGMALHRVVSFYTV

Parental  G
          G
Retrocopy G

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_630 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_630 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013726	1 retrocopy	retro_cfam_1092,
Myotis lucifugus	ENSMLUG00000015241	2 retrocopies	retro_mluc_1399, retro_mluc_2012,
Monodelphis domestica	ENSMODG00000017305	1 retrocopy	retro_mdom_1534,
Ochotona princeps	ENSOPRG00000002758	1 retrocopy	retro_opri_1003,
Vicugna pacos	ENSVPAG00000011819	1 retrocopy	retro_vpac_630 ,