RetrogeneDB ID: retro_pcap_295

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_280120:434..923(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG2
• Ensembl ID: ENSPCAG00000011588
• Aliases: None
• Description: BCL2-associated athanogene 2 [Source:HGNC Symbol;Acc:938]

Sequence

>retro_pcap_295
ATGTACCGGGGGAAGATATAGGAAAAAGACAATGTGGGGTGCTTCCCCTGCTCCCTTCTATGGCCCACTGCTCCAGCCAC
CTACTGGAGAGCCTGGACCAGCTGGAGCTCAGGTTTGAAGTTTTGAGAGAAGCAGCAAGGGCCTGCTGAGCAAAATAAGT
AAATTCTCTTGAAAATGACCCATGATATGCAAAATAACCAGAACATGAGGTAGATCAGTGATGGAGCCAGAGAATTATAT
CTGACTACAAACAATTCGATGGGACAAACCCTCGGTGCTGAAGTTTCAGTAGAAACAATTAGAAGCCCCTAGTAGTAAGA
ATCCCTAGAGCATGTCACCAGTATTATTGATGAGGTGGTCAGCATGCTTCTGGGTGATTTGGAAAATGCCGTCATTTAAT
GGCAGTGTAAAAATGTTTGTTCTTCTAAGGTACCAGCTGGGCCAGTTGATCAGAAGTTTCGGCCTATAGCAATTGTCTGT
GCTTTTGAA

Alignment

ORF - retro_pcap_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAQAKINAKANEGRFCRS-SSMADRSSRLLESLDQLELRVEALREAASAI-EQEKEILLEMIHSIQNSQD
          M...KI..K.N.G.F..S..SMA..SS.LLESLDQLELR.E.LREAA.A..EQ.K.ILL.M.H..QN.Q.
Retrocopy MYRGKI*EKDNVGCFPCS<PSMAHCSSHLLESLDQLELRFEVLREAARAC>EQNK*ILLKMTHDMQNNQN

Parental  MRQISDGEREELNLTANRLMGRTLTVEVSVETIRNPQQQESLKHATRIIDEVVNKFLDDL-GNAKSHLMS
          MR.ISDG.RE.L.LT.N..MG.TL..EVSVETIR.P...ESL.H.T.IIDEVV...L.DL.G....HLM.
Retrocopy MR*ISDGARE-LYLTTNNSMGQTLGAEVSVETIRSP***ESLEHVTSIIDEVVSMLLGDL<GKCR-HLMA

Parental  L-YSACSSELPPGPVDQKFQSIVIGCALE
          .....CSS..P.GPVDQKF..I.I.CA.E
Retrocopy V>KNVCSSKVPAGPVDQKFRPIAIVCAFE

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_295 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
Canis familiaris	ENSCAFG00000028759	1 retrocopy	retro_cfam_252,
Myotis lucifugus	ENSMLUG00000004055	1 retrocopy	retro_mluc_251,
Oryctolagus cuniculus	ENSOCUG00000004815	1 retrocopy	retro_ocun_823,
Procavia capensis	ENSPCAG00000011588	1 retrocopy	retro_pcap_295 ,