RetrogeneDB ID: retro_pcap_116

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_6922:50463..51142(-)
• Located in intron of: ENSPCAG00000013508

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP4
• Ensembl ID: ENSPCAG00000011030
• Aliases: None
• Description: retinoblastoma binding protein 4 [Source:HGNC Symbol;Acc:9887]

Sequence

>retro_pcap_116
TTTGATGCATCACACTGCAACAACGAGAAAGGAGAATTGGGAGGGTTTGGTTCAGTTAGTGGAAAGATTGAAATAGAAAC
CAAGATCAATCATGAAGAAGAAAACAGGTTCATTATATGCCCCAGAACTTTTGCATCATTGCAGCAAAGATTCCATCCAG
TGATGTTCTTGTTTTTGACTATACCAAACACCCTTCTAAACCAGACCCTACTGGAGATTACAACACAGACTTGCATCTCT
GTTGACATCAGAAGGAAGGCTATGGAGTTTCTTGAAACTCAAGTCTCAGGGGGCCACTTCTGCTTCAAATGACCATACCA
TCTGCCTGTGGGAACATCAGTGCTGTTTCAAAGAAGGAAAAGATATAGATGTAAAGATCATCTTTTCTGGACGTACAGCA
ATATTTGAAGATGTTTTCTGGTAACTGTTTCATGAATATCTGTTTGGGTAAGTTGCTGATGATCAGTTTATGATCTGGGA
TACTTGTTCAAACACTCCTTCCAAACCAAGTTGCTCAGTTGATGCTCACACTGCTACAGTGATCTGCCTTTATTTCAGTC
CTTATAATGGATTCATTCTTGTCCCAGGATCAGTTGACAAGACTGTTGCTTTTTGGGACTTGAGAATTCTGAAACTCCAG
TTGCCTTCCTTTGAATCACATAAAGATATAATATTCCAG

Alignment

ORF - retro_pcap_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.83 %
• Parental protein coverage: 56.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNR-ARYMPQNPCIIATKTPSSDVLVFDYTKHPSKP
          FDASH...EKGE.GGFGSVSGKIEIE.KINHE.E.NR...YMPQN.CIIA.K.PSSDVLVFDYTKHPSKP
Retrocopy FDASHCNNEKGELGGFGSVSGKIEIETKINHEEE-NR<VHYMPQNFCIIAAKIPSSDVLVFDYTKHPSKP

Parental  DPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLL-SASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVV
          DP.G..N.DL.L..HQKEGYG.S.N..L.G.LL....D.HTICLW......KEGK..D.K.IF.G.TA..
Retrocopy DPTGDYNTDLHLC*HQKEGYGVS*NSSLRGPLL<ASND-HTICLWEHQCCFKEGKDIDVKIIFSGRTAIF

Parental  EDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVAL
          EDV.W.L.HE.LFG.VADDQ..MIWDT.SN..SKPS.SVDAHTA.V.CL.F.PY..FIL..GS.DKTVA.
Retrocopy EDVFW*LFHEYLFG*VADDQ-FMIWDTCSNTPSKPSCSVDAHTATVICLYFSPYNGFILVPGSVDKTVAF

Parental  WDLRNLKLKLHSFESHKDEIFQ
          WDLR.LKL.L.SFESHKD.IFQ
Retrocopy WDLRILKLQLPSFESHKDIIFQ

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_116 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 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001021	7 retrocopies	retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus	ENSCPOG00000015352	3 retrocopies	retro_cpor_154, retro_cpor_27, retro_cpor_899,
Macaca mulatta	ENSMMUG00000009940	1 retrocopy	retro_mmul_75,
Monodelphis domestica	ENSMODG00000017415	6 retrocopies	retro_mdom_1542, retro_mdom_1833, retro_mdom_1873, retro_mdom_1900, retro_mdom_563, retro_mdom_765,
Mustela putorius furo	ENSMPUG00000015214	1 retrocopy	retro_mputfur_104,
Procavia capensis	ENSPCAG00000011030	1 retrocopy	retro_pcap_116 ,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Rattus norvegicus	ENSRNOG00000021492	1 retrocopy	retro_rnor_1270,
Sarcophilus harrisii	ENSSHAG00000010923	1 retrocopy	retro_shar_399,