RetrogeneDB ID: retro_pcap_234

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_201062:483..1308(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000001718
• Aliases: None
• Description: None

Sequence

>retro_pcap_234
ATCTTTCCATTCCTCACTCCAATTTTTGAAGTATTAAATATCTCTGTGTTTCCAAGAGCTCCTACTGACTTTTTCACAAA
ATCTGTACAAACAATAAAAGAAAATCGCCTTAAAGATAATAAAAAGCACCGAGTGGCTTTTCTTCAGCTGATGATTGACT
CCCAGACGTCAAAAGAAACTGCATCCCATAAAGCTTTGACAGATACGGAGCTTGTAGCCCTATCAATTATGTTCATTTTT
GCTGGCTATGAGACCACTAGCACCACTCTTTCCTTCCTTATGTACTCATTGGCCACTCACCCTGATATTCAGCAGAAACT
ACAGAAGGAGATTGATGCAGCTTTGCCCAATAAGGCATCTCCCACATATGATGTCACATTACAGATGGAATATCTTGACA
TGGTGGTGAATGAAACACTCAGATTATTCCCAATTGTTGGCAGACTTGAGAGACTATGTGAGAAAGATGTTGAAATCAAT
GGACTGATCATTCCCAAAGGTGCGGGGGTGATAGTGACAGTCTTTGTTCTCCACCGAGACCCAGAACACTGGCCAGAGCC
TGAGAAATTCCTTCCTGAAAGGTTCAGTAAGGAGAATAAGGACAACATAGACCCTTACTTATACCTGCCCTTTGGAAGTG
GACCCCGAAATCGCATTGGCATGATGTTTGCTCTCATGAACACGAAACTGGCTGTCATCAGAATTCTGCAGGAGTTCTCT
GTCAAACTTTGTAAAGAAACACAGATCCCCCTAAAATTAGGCAAGAAAGTACTCACTGCACCAGAAGTACCTGTTGTTTT
AATGTTTGAACCAAGAGATGGAAAT

Alignment

ORF - retro_pcap_234 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.0 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFPFLIPICDAFHISVFSRDVTDFLTKSIQRMKESRLKDKEKYRVDLLQLMIESQNSKETASYKALTDTE
          IFPFL.PI.....ISVF.R..TDF.TKS.Q..KE.RLKD..K.RV..LQLMI.SQ.SKETAS.KALTDTE
Retrocopy IFPFLTPIFEVLNISVFPRAPTDFFTKSVQTIKENRLKDNKKHRVAFLQLMIDSQTSKETASHKALTDTE

Parental  LVAQSIVFIFAGYETTSTALSFLMYLLATHPDIQQKLQKEIDEALPNKAPPTYDNVFQMEYLDMVVNETL
          LVA.SI.FIFAGYETTST.LSFLMY.LATHPDIQQKLQKEID.ALPNKA.PTYD...QMEYLDMVVNETL
Retrocopy LVALSIMFIFAGYETTSTTLSFLMYSLATHPDIQQKLQKEIDAALPNKASPTYDVTLQMEYLDMVVNETL

Parental  RIFPVASRVERICKKDIEINGVIIPKGTVVMVPIFVLHRDPENWPEPEKFLPERFSKKNKDNINPYLYLP
          R.FP...R.ER.C.KD.EING.IIPKG..V.V..FVLHRDPE.WPEPEKFLPERFSK.NKDNI.PYLYLP
Retrocopy RLFPIVGRLERLCEKDVEINGLIIPKGAGVIVTVFVLHRDPEHWPEPEKFLPERFSKENKDNIDPYLYLP

Parental  FGNGPRNCIGMRFALMNMKLAVIRILQEFSVKTCKETQIPIKLGKAIVISPEGSIVTRFESRDGS
          FG.GPRN.IGM.FALMN.KLAVIRILQEFSVK.CKETQIP.KLGK.....PE...V..FE.RDG.
Retrocopy FGSGPRNRIGMMFALMNTKLAVIRILQEFSVKLCKETQIPLKLGKKVLTAPEVPVVLMFEPRDGN

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_234 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035708	1 retrocopy	retro_cjac_1135,
Procavia capensis	ENSPCAG00000001718	1 retrocopy	retro_pcap_234 ,
Ictidomys tridecemlineatus	ENSSTOG00000028864	1 retrocopy	retro_itri_1559,