RetrogeneDB ID: retro_pcap_370

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_52587:1149..1798(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSPCAG00000005623
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_pcap_370
AAGTCCAGATTCAGAAATATTTCACCTTCAACTGTGTTCATCAAAAGGTTTCTTAGACCTATCTGTAATGTACACTGTGG
CAGAATTGAATAAAGTCAACCAGGCTGGCAATGATGAGTGTACTTTTGGAACAAGGACATTTTTGCAGTCAATGGAAGGA
CGCCAGTACTTATACCACCTTCAGCTCAAGCAGGAATTTATGGATAAAATTAGTACCATTTGGGGACTGACAAAAATGGG
AAAATTGGATATAGTGTGGAAAAGAAATCTAGGTGAAATGGCACTGCTTTACACAACCCAACTTGAAAGAGAAGTTCCAC
GATACAGAAATTTGAGGTTGTCTCTAGAGACAATTCCAGATACTGTAATTCTAGAAGAGCCTTTTCATATTACCTGTAAG
ATAACAAACTGCAGTAAGAGGAAAATGAAACTGATCTTGACAATGAGTGATACAGATTCTGTTCATTGGTGTGGATGTTC
AGGAAGGTGTCTTGGAAAGCTGCCTCCAGGTTCATCTCTCTGCTTTACACTCACACTACTCTCCTTGAAACTGGGCCTGC
AGAGTATCTCTGGCATACAAATAACAGATAAATTATTAAGAAGAACATATAAACATGTTGATGTTGCGAAAGTCTATGTA
ATATCTTCC

Alignment

ORF - retro_pcap_370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.25 %
• Parental protein coverage: 61.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAQIQNITNSPMFM-EKVS-LEPSIMYSVAELNSVSQAGECLSTFGSRAYLQPMDTRQYLYCLKPKKEFA
          .....NI..S..F...KVS.L..S.MY.VAELN.V.QAG....TFG.R..LQ.M..RQYLY.L..K.EF.
Retrocopy KSRFRNISPSTVFI<QKVS<LDLSVMYTVAELNKVNQAGNDECTFGTRTFLQSMEGRQYLYHLQLKQEFM

Parental  EKAGIIKGVTVIGKLDIVWKTNLGERGRLQTSQLQRMXXXXXXXXXXXXXXPDTVNLEEPFHITCTFTNC
          .K...I.G.T..GKLDIVWK.NLGE...L.T.QL.R...............PDTV.LEEPFHITC..TNC
Retrocopy DKISTIWGLTKMGKLDIVWKRNLGEMALLYTTQLEREVPRYRNLRLSLETIPDTVILEEPFHITCKITNC

Parental  SERTMDLVLEMCNTNSIHWCGISGRQLGKLHPSSSLCLALTLLSSVQGLQSISGLRLTDTFLKRTYEYDD
          S.R.M.L.L.M..T.S.HWCG.SGR.LGKL.P.SSLC..LTLLS...GLQSISG...TD..L.RTY...D
Retrocopy SKRKMKLILTMSDTDSVHWCGCSGRCLGKLPPGSSLCFTLTLLSLKLGLQSISGIQITDKLLRRTYKHVD

Parental  IAQVCVVSS
          .A.V.V.SS
Retrocopy VAKVYVISS

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_370 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
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Otolemur garnettii	ENSOGAG00000010787	1 retrocopy	retro_ogar_3287,
Procavia capensis	ENSPCAG00000005623	1 retrocopy	retro_pcap_370 ,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,