RetrogeneDB ID: retro_pcap_261

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_237829:81..1080(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHB
• Ensembl ID: ENSPCAG00000016595
• Aliases: None
• Description: pyruvate dehydrogenase (lipoamide) beta [Source:HGNC Symbol;Acc:8808]

Sequence

>retro_pcap_261
TCTGGGCTGCTGAGGGGGTGCTTCCACCAGAAGGGACCAGCGGCACTGCAGGTAACAGTTCATGATGCTCTAAATCAAGG
GATGGACAAGGAGCTACAAACAGATGAGGTTTTTATGCCGGGGGAGGAAGTTGCCTGGGATGATGGGACATACAGGGTTA
GTTGAGGGCTATGGAACAAATATGGAGACAAGAGGATCACAGACACTTCCGTATCTGAGATGGACTTTGCTGGAATTGCT
GTAAGGTATAGCTGTGGCTGGGTTGTGGCCTATTTGTGAATTTATGACCTTTCATCTCTCTATGCAAGCCATTGAGCAAG
TTACCAAGTTGGCTGCCAAGACCTACTACATGTCCAGAAGCCGTCAGTCTGTGCCTATTGTCTTCAAGGAGCCTAATGGT
GCCTCCATGGGTGTGCCTGCTTGGCACTTGCAGTGCTTTCTTGCCTGGTACAACACTGCCCAGCTTAAAGGTGGTCAGAC
CATGGAAATGAGAGGATCTAAAACAACTTATTAAATCAGTCATTCAGGACAACAGTCCAGTGGTGATGTTGAAGAATGAA
CAGATGTATGGGTTCCTTTTGAATTTCCTGATGCAGATCATTCAAAAGACTTCCTGATTCCTATTGGAAAAGCCAAAATA
GAAAGGCAAGGGATGCATGTGACCGTGGTTTCCCATTCAAGATCTCTTGGCCACTGTTTAGAAGCTGTGGCAGCCCTATC
TAAAGAGGGAATTGAATGTGTGGCAATAAATACATGTACCATCAGGCCAATTAACATTGAAATCATGGAAGCCAATGTCA
TCAAGACAAACCACCTTGTGACCGTGGAAGGAGGCTGGCCACAGTTTGGAGTAGGAGCTGAAATTTGTGCCAAGATCATG
GATGCTTACCTGGATGCTCCTGCAGTTCCTGTCATTGGTATTGATGTCGCTGTCCCTTACACAAAGATTCTGAACACAGC
TTTGTACCACAGGTCAAAGACATCATGTTTTCAATAAAG

Alignment

ORF - retro_pcap_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.22 %
• Parental protein coverage: 94.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SGLLRRHFHRTAPAALQVTVRDAINQGMDEELERDEKVFLLGEEVAQYDGAYKVSRGLWKKYGDKRIIDT
          SGLLR..FH...PAALQVTV.DA.NQGMD.EL..DE.VF..GEEVA..DG.Y.VS.GLW.KYGDKRI.DT
Retrocopy SGLLRGCFHQKGPAALQVTVHDALNQGMDKELQTDE-VFMPGEEVAWDDGTYRVS*GLWNKYGDKRITDT

Parental  PISEMGFAGIAV-GAAMAGLRPICEFMTFNFSMQAIDQVINSAAKTYYMSGGRQPVPIVFRGPNGASACV
          ..SEM.FAGIAV.G.A.AGL.PICEFMTF..SMQAI.QV...AAKTYYMS..RQ.VPIVF..PNGAS..V
Retrocopy SVSEMDFAGIAV>GIAVAGLWPICEFMTFHLSMQAIEQVTKLAAKTYYMSRSRQSVPIVFKEPNGASMGV

Parental  AAQHSQCFAAWYG-HCPG-LKVVSPWNAEDAKGLIKSAIRDNNPVVMLENELMYG-VPFEFPEAAQSKDF
          .A.H.QCF.AWY..HCP..LKVV.PW..ED.K.LIKS.I.DN.PVVML.NE.MYG.VPFEFP.A..SKDF
Retrocopy PAWHLQCFLAWYN<HCPA<LKVVRPWK*EDLKQLIKSVIQDNSPVVMLKNEQMYG<VPFEFPDADHSKDF

Parental  LIPIGKAKIERPGTHVTLVSHSRPVGHCLEAATVLSKEGIECEVINMRTIRPMDIETIEASVVKTNHLVT
          LIPIGKAKIER.G.HVT.VSHSR..GHCLEA...LSKEGIEC..IN..TIRP..IE..EA.V.KTNHLVT
Retrocopy LIPIGKAKIERQGMHVTVVSHSRSLGHCLEAVAALSKEGIECVAINTCTIRPINIEIMEANVIKTNHLVT

Parental  VEGGWPQFGVGAEICAKIMEGPAFNYLDAPAVRVTGADVPMPYAKIL-EDNSVPQVKDIIFAVK
          VEGGWPQFGVGAEICAKIM......YLDAPAV.V.G.DV..PY.KIL.E...VPQVKDI.F..K
Retrocopy VEGGWPQFGVGAEICAKIMDA----YLDAPAVPVIGIDVAVPYTKIL<EHSFVPQVKDIMFSIK

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_261 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261 ,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,