RetrogeneDB ID: retro_pcap_126

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7635:104850..105340(-)
• Located in intron of: ENSPCAG00000018823

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX4
• Ensembl ID: ENSPCAG00000014587
• Aliases: None
• Description: syntaxin 4 [Source:HGNC Symbol;Acc:11439]

Sequence

>retro_pcap_126
GACAGGACCCATGAGCTGAGGCAGGGAGAAGAGAGCTGGCACGATGAGGACAAGGGGCAGGTCATGTTGGTGCCTTACCG
GAGCACGGCCTAATTACGGAGCTCGGACGATGAGTCCTTCCAGAAGGAGAAGACAATTCTGCAGACTATTATCAAGTTTA
AGAATAAAGTCAAGGAGTTGGAGAAGCAGCAGGTTAGCATCCTGGACGTGCCTTTGCCTAGGAGACTATGAAGCAGAACC
TGCGTGCAGAGATCAGACACCTGGGGAGGGAATGCTGCACTCAACTGCCGGCCATAGAGCCCCAAAAGAGGAAGCTGATG
AGAATTATAACCCAGTCAACACAAAGATGAGAAAAACCCAGCGTGAGGTCTTATCTCAGCAATTCACGGATCTTATCAAT
AAGCACAACTTGATGCAGTCTGAATGCCAAGAGGAGAATGTGGAGTAGATTCTGAGGCAGCTGAAGATCACCCTTGCTGG
AATGGTATCT

Alignment

ORF - retro_pcap_126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 56.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRTHELRQGDDSSDDENKERVALVVHPGTARLGSPDDEFFQKVRTIRQTIVTLENKVRELEKQQVTILAT
          DRTHELRQG..S..DE.K..V.LV....TA.L.S.DDE.FQK..TI.QTI....NKV.ELEKQQV.IL..
Retrocopy DRTHELRQGEESWHDEDKGQVMLVPYRSTA*LRSSDDESFQKEKTILQTIIKFKNKVKELEKQQVSILDV

Parental  PLPE-ESMKQDLQNLREEIKQLGREIRTQLKAIEPQ-KEEADENYNSVNTRMRKTQHGILSQQFVDLINK
          PLP..E.MK...QNLR.EI..LGRE..TQL.AIEPQ.KEEADENYN.VNT.MRKTQ...LSQQF.DLINK
Retrocopy PLPR<ETMK---QNLRAEIRHLGRECCTQLPAIEPQ<KEEADENYNPVNTKMRKTQREVLSQQFTDLINK

Parental  CNLMQSEYREKNVERIRRQLKITNAGMVS
          .NLMQSE..E.NVE.I.RQLKIT.AGMVS
Retrocopy HNLMQSECQEENVE*ILRQLKITLAGMVS

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_126 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000014587	1 retrocopy	retro_pcap_126 ,