RetrogeneDB ID: retro_pcap_294

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_279126:195..1021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: P2RY11
• Ensembl ID: ENSPCAG00000007303
• Aliases: None
• Description: purinergic receptor P2Y, G-protein coupled, 11 [Source:HGNC Symbol;Acc:8540]

Sequence

>retro_pcap_294
CTGATGCTCAACAGCTTCAGCCCCCATGACATGCAGGTGAAACTCATGGCCACTGTATCCCAGAACTTGTTGCCCCTCCA
TAGACATGCACTAGTTAAATCTGAACACCACCAAGTGCTACCTCCTTATCAACTACAACCCCACTCCCTGTATCTGGATT
TCTGCCATTATATCATCAAAGTTGTACTGTATGACCAAGTGGCAAGATGAAGATGCTTCCCCAGCAGAAGTTTCCCAATA
TGAGTTGTTTGCAGGGTTTCAGGGAACTACTGCCCATAGGTAAGATGCTGTCACAGAGCAAGGTAGAGCCTGCAGTTGAA
CACAATATAAAGGTGATGCTCCAGGCCATCCCTAGGCACTGTAAAATGCAGACCCAGCAGAGCACCTTGCAACGTACTGA
GATGGGTCCTCAGATGATACTGTAGCTCATCAAGATACAGAAGGGTGCCTGGGAGGGAACGTGTTTTTCCAGTTTCCCAC
ACATGGTTGAGGAGGAGTCTCAGGTCATCCTGGTGGTCAAGGAAGAGAGGCTACAGCTGAAAGTCCAGAGGCAGGATCAG
CAGGTCCATACTGCGCTGCACCAGCAAAAGATGGGCAGTCAGGAAGAGGGCACAGTCAGGTGGATAAGGTCAGTGATAGT
GAGGACCAGAGGCCCACAAGAGACAGGGAGGAGTGGCCAACCTAAGGAGGAGGATGAAGTTGAGTATTCCTACCACACAG
TACGCAGAGAACCTGATGAGTACATGTTCTTGAGATTGACCAAGCAGAGACAGCACACAGGTATCCACACAAGAAGCAGT
CGGTAAAGGATCAGAGGCCAGACCAG

Alignment

ORF - retro_pcap_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.93 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVLNSFGPHGMHVKLMATMFQNLFP-SINVHKVNLNTIKRCLLINYNP-ESQELDFRHYSIKVV-PVGAS
          L.LNSF.PH.M.VKLMAT..QNL.P.SI..H..NLNT.K..LLINYNP..S..LDF.HY.IKVV..V..S
Retrocopy LMLNSFSPHDMQVKLMATVSQNLLP>SIDMH*LNLNTTKCYLLINYNP<HSLYLDFCHYIIKVV<TV*PS

Parental  RGMKKLLQEKFPNMSRLQDISELLATGAGLSESEAEPDGEHNIAELPQAVAGRGNMRAQQSAVRLTEIGP
          ..MK.L.Q.KFPNMS.LQ...ELL..G..LS.S..EP..EHNI....QA......M..QQS....TE.GP
Retrocopy GKMKMLPQQKFPNMSCLQGFRELLPIGKMLSQSKVEPAVEHNIKVMLQAIPRHCKMQTQQSTLQRTEMGP

Parental  RMTLQLIKIQEGVGEGNVLFHSFVHKTEEELQAILAAKEERLRLKAQRQDQQAHNVQRKREQREAHRKSL
          .M.L.LIKIQ.G..EG...F.SF.H..EEE.Q.IL..KEERL.LK.QRQDQQ.H................
Retrocopy QMIL*LIKIQKGAWEG-TCFSSFPHMVEEESQVILVVKEERLQLKVQRQDQQVHTALHQQKMGSQEEGTV

Parental  -CMKRLRAKADGDSDAEDPGAPPENDGEEDEAEYFRQAVGEEPDEDMFPELTKRRQPI-RPPHKKQRVKD
          ...........G.......G.P.E....EDE.EY....V..EPDE.MF..LTK.RQ...R.PHKKQ.VKD
Retrocopy RWIRSVIVRTRGPQETGRSGQPKE----EDEVEYSYHTVRREPDEYMFLRLTKQRQHT<RYPHKKQSVKD

Parental  RRPDQ
          .RPDQ
Retrocopy QRPDQ

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_294 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000007303	1 retrocopy	retro_pcap_294 ,