RetrogeneDB ID: retro_pcap_2

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_42640:3021..4554(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000012277
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000006667
• Aliases: None
• Description: None

Sequence

>retro_pcap_2
GCAAGGCCAGAGATTCATCCGTGTCCCCCCTGCCTTCTGGCCTTCTCCACTCAGAAATTCCTCAGCCACCACGTGAAGCA
CAGCCACCGCCATCAGCCCTTCCCAGGAACTCCTACAAGAAGACCCCTCCAACCAGAGGACCACCATCCAGGGGATCGGA
GGCAGCAGCATTCTGAGCAACAGAACTGGAATGACAAAGCTGAAGGTCCAGAGATAGGACATGTGTCCAGACTAGTGTTT
GAAAAGGCAAGACAGGAGGGGATTTCACAGGCCGGCTCCAGCCTCCCCAAAGGGCAGATAGGGCGGTCTAGGGATGGGGA
GAGAACCACGGAGACAGAGAGCAGCCCAGGCCTGAAGGTGAATCCTGAGGACACAGAGACATTGTTCCTGAGGGGAGGAA
TCTCAAAAATTGCAAAAGTCAACTGTGGAGAATGTGGACAAGGCTTTAGTTGGAAATCACGCCTCATCAGATACCAGAGG
ACACACTCAGGGGAGAAGCCCTGTGTCTGCAGGGAGTGTGGGCGGAGATTTAGTTGCAAGTCAGTCCTCCTCCGACACCA
GAGGACACACTCAGGGCAGAAGCCCTATGTATGCAAGGAGTGTGGGCGAGGCTTTAGCTGGAAGTCAAACGTTATCATAC
ACGAGAGGACACACTCAGGAGAGAAGCCCTATGTGTGTAGGGAGTGTGGGCGAGGGTTTAGTTTAAAGTCATACCTCATC
ACACACCAGAGGACACACTCAGGGGAGAAGCCCTATGTCTGCAGGGAGTGTGGGCGAGGCTTTAGTCACAGGTCACACCT
CATCACACACCAAAGGACACACTCAGGGGAGAAGCCCTATGTCTGCAGGGAGTGTGGGCGAGGTTTTAGTGATAAGTCAG
GCATCATCCGACACCAGAGGATACACTCAGGGGAGAAGCCCTATGTCTGCAGGGAGTGTGGGCGAGGCTTTAGTGTCAAG
TCGCGCCTCATCCGACACCAGAAGTCACACACAGGGGAGAAGCCCTTTGTCTGCAGGGAGTGTGGGCGAGGCTTTAGTGA
AAAGTCAGGCCTCATCAGACACCAGAGGACACACTCGGGGGAGAAGCCCTACGTATGCAGGGAGTGTAGGCGAGGCTTTA
GTGTCAAGTCACAGCTCATCCGACATCAGAGGTCACACTCAGGGGAGAAGCCGTATGTCTGCAGGGACTGTGGGCGAGGC
TTTAGTCAAAAGTCAGGCCTCATCCGACACCAGAGGACACACTCAGGGGAGAAGCCGTATGTGTGCAGAGAGTGTGGGCG
AGGCTTTAGTGTGAAGTGCCACCTCATCCGACACCAGAGGACACACTCTGGGGAGAAGCCTTATGTCTGCAGGGAGTGTG
GCCGAGGCTTTAGTCAAAAGTCAGGCCTCATCACACACCAGAGGACACACTCGGGGGAGAAGCCCTATGTCTGCAGGCAG
TGTGGGCGAGGCTTTAGTCAAAAGTCAGGCCTCATCCAACACCAGAGGAGACACTCAGGGGAGAAGCCCTATGTCTGTAG
GGAGTGTGGGCAA

Alignment

ORF - retro_pcap_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARPEIHPCPPCPLAFSTPKFLSHHVKHSHRRQPFPGTPTRRPLQPEDPHPRDRRQQHSQQPNWNDKAEGP
          ARPEIHPCPPC.LAFST.KFLSHHVKHSHR.QPFPGTPTRRPLQPED.HP.DRRQQHS.Q.NWNDKAEGP
Retrocopy ARPEIHPCPPCLLAFSTQKFLSHHVKHSHRHQPFPGTPTRRPLQPEDHHPGDRRQQHSEQQNWNDKAEGP

Parental  EIGRVSRPVFERARQEGISEAGSSLPKGQMGQSRDGERTTETESSPGLKVNPEDTETLFLRGGISEIAKV
          EIG.VSR.VFE.ARQEGIS.AGSSLPKGQ.G.SRDGERTTETESSPGLKVNPEDTETLFLRGGIS.IAKV
Retrocopy EIGHVSRLVFEKARQEGISQAGSSLPKGQIGRSRDGERTTETESSPGLKVNPEDTETLFLRGGISKIAKV

Parental  NCGECGQGFSWKSRLIRYQRTHSGEKPCVCRECGRGFSVKSRLIRHQKSHSGEKPYICRDCGQGFSQKSG
          NCGECGQGFSWKSRLIRYQRTHSGEKPCVCRECGR.FS.KS.L.RHQ..HSG.KPY.C..CG.GFS.KS.
Retrocopy NCGECGQGFSWKSRLIRYQRTHSGEKPCVCRECGRRFSCKSVLLRHQRTHSGQKPYVCKECGRGFSWKSN

Parental  LIRHQRTHSGEKPFVCRECGRGFSEKSSLIRHQRTHSGEKPYVCRDCGRGFSQKSGLIRHQRTHSGEKPY
          .I.H.RTHSGEKP.VCRECGRGFS.KS.LI.HQRTHSGEKPYVCR.CGRGFS..S.LI.HQRTHSGEKPY
Retrocopy VIIHERTHSGEKPYVCRECGRGFSLKSYLITHQRTHSGEKPYVCRECGRGFSHRSHLITHQRTHSGEKPY

Parental  VCRECGRGFSVKCHLIRHQRTHSGEKPYVCRECGRGFSQKSGLITHQRTHSGEKPYVCRQCGRGFSQKSG
          VCRECGRGFS.K...IRHQR.HSGEKPYVCRECGRGFS.KS.LI.HQ..H.GEKP.VCR.CGRGFS.KSG
Retrocopy VCRECGRGFSDKSGIIRHQRIHSGEKPYVCRECGRGFSVKSRLIRHQKSHTGEKPFVCRECGRGFSEKSG

Parental  LIQHQRTHSGEKPYVCRECGQCFSGKTHLVTHQRTHSGEKPYVCRECGRGFSQKSGLITHQRTHSGEKPY
          LI.HQRTHSGEKPYVCREC...FS.K..L..HQR.HSGEKPYVCR.CGRGFSQKSGLI.HQRTHSGEKPY
Retrocopy LIRHQRTHSGEKPYVCRECRRGFSVKSQLIRHQRSHSGEKPYVCRDCGRGFSQKSGLIRHQRTHSGEKPY

Parental  VCRQCGRGFSQKSGLIQHQRTHSGEKPYVCRECGRGFSQNSSLIQHQRTHSREKLYVCRECGRGFSVRYS
          VCR.CGRGFS.K..LI.HQRTHSGEKPYVCRECGRGFSQ.S.LI.HQRTHS.EK.YVCR.CGRGFS....
Retrocopy VCRECGRGFSVKCHLIRHQRTHSGEKPYVCRECGRGFSQKSGLITHQRTHSGEKPYVCRQCGRGFSQKSG

Parental  LMNHQRAHSGEKP--CGECGQ
          L..HQR.HSGEKP..C.ECGQ
Retrocopy LIQHQRRHSGEKPYVCRECGQ

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_2 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	ENSPCAG00000006667	1 retrocopy	retro_pcap_2 ,