RetrogeneDB ID: retro_pcap_280

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_257438:581..1217(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALG14
• Ensembl ID: ENSPCAG00000014267
• Aliases: None
• Description: ALG14, UDP-N-acetylglucosaminyltransferase subunit [Source:HGNC Symbol;Acc:28287]

Sequence

>retro_pcap_280
ATCGAGGGTACCTTTATTCTAGCAGCGCTCGGAGGAGGAATGGTGGCCGTCTTCGCAGTACTGTGGCTTTGAGCAGTGCT
TCATCGTCGAGTGGTGTCTTGTGACTCAGTCTTTTGGTAGTCGCCAGGTCCGGTGGACACACCACTGAAGTCCTAAGACT
GGTTGTGAGACTCTCTGATGCTTACTCTCCAAAGCATTATATCTTTGCTGACACGGGTGAGATGAGTGCCCATAAAATAA
AAGCTTTTGAACGAGATGGAGCTAAGAAATACTCTACTACCAAATATACCACTGACCAAAACCCAAGAAGCCGCGAGGTG
TGGCAGTCCTGGGTCTCCACAGTACTCACCACCCTGTACTCCATGCTGTATTCCTTGCCCCCTGACTTTCAGACTGAAGC
CGGATTTGGTGTTGTGTAATGGACCACGAACATGTGTTCCTATCTACATATCTGCCCTCCTCCTTTGGATACTAGGAATA
AAGAAAGTGATCACTGTCTATGTTGAAAGTGTCTGCCGAGTGGAAACTTTAGCCCTGTCCGGAACGATTCTGTGCTACCT
CTCAGATTACTTCATTTTTCAGTGGCCCACTCTTAAGGAGAAGTATCCCAAATCTGTGTACCTGGGGTGAATTGTT

Alignment

ORF - retro_pcap_280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEGALILAALGGGTMAVYLLLRLWVVGH-FVVSRESL-SLLLVAAGGHTTEILRLVGSLSDAYSPRHYVF
          .EG..ILAALGGG..AV...L.L..V.H..VVS..S...L.....GGHTTE.LRLV..LSDAYSP.HY.F
Retrocopy IEGTFILAALGGGMVAVFAVLWL*AVLHRRVVSCDSV<LLVVARSGGHTTEVLRLVVRLSDAYSPKHYIF

Parental  ADTDEMSAHKIKAFELDRAKRYSTTMYTTDRIPRSREVQQSWLSTVLTTVYSMLYSF-PLTFKLKPDLVL
          ADT.EMSAHKIKAFE.D.AK.YSTT.YTTD..PRSREV.QSW.STVLTT.YSMLYS..PLTF.LKPDLVL
Retrocopy ADTGEMSAHKIKAFERDGAKKYSTTKYTTDQNPRSREVWQSWVSTVLTTLYSMLYSL>PLTFRLKPDLVL

Parental  CNGPGTCVPICISALLLGILGVKKVIIVYVESVCRVETLSLSGKILYYLSDYFIVQWPTLKEKYPKSVYL
          CNGP.TCVPI.ISALLL.ILG.KKVI.VYVESVCRVETL.LSG.IL.YLSDYFI.QWPTLKEKYPKSVYL
Retrocopy CNGPRTCVPIYISALLLWILGIKKVITVYVESVCRVETLALSGTILCYLSDYFIFQWPTLKEKYPKSVYL

Parental  GRIV
          G.IV
Retrocopy G*IV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_280 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008564	1 retrocopy	retro_dord_482,
Procavia capensis	ENSPCAG00000014267	1 retrocopy	retro_pcap_280 ,
Ictidomys tridecemlineatus	ENSSTOG00000025476	1 retrocopy	retro_itri_1820,
Tursiops truncatus	ENSTTRG00000016557	1 retrocopy	retro_ttru_88,