RetrogeneDB ID: retro_pcap_358

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_48406:11666..12502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT8
• Ensembl ID: ENSPCAG00000007178
• Aliases: None
• Description: septin 8 [Source:HGNC Symbol;Acc:16511]

Sequence

>retro_pcap_358
TCCCACATCCATGTGAAACTTTACTTCATTATAGTTGCTGACCACTCTCTGAAAACACTTAATCTTTTGACCATGAAAAA
CATTGACATTAAGGTAAACATTATTCCAGTGATTGTCCAAGCAGATGCAGTTTCTAAAACTGAATTACTCAAATTTAGGA
TCAAGCTCATGAGTAAATTGATTAGCAATGTCATCCAGATATACCAGTTCCTAAGAGATGATGACACTACTGCTAAAATC
AATTCTTCAACGAATGCACACGTGCCGTTTGCTGTTGTAGGAAGTGTGGATGAGGTCAAAGTCAGAATGAGGGTGACCAA
AGCTTGTCAGTATCCTTGGAGTGTTGTACAAGTGGAAAATGGAAACCACTGTGACTTTGTAAAGTCACAGGAAATGCTAA
TTTGTACAAAAATGGAAGATCAACAAGAACAAATGCACATTTGACATTGTGAACTTTACAGATTTTGCAAACTGAAAGAA
TTGGGTTTGAAACATGTGGGCTCAGTCTACAAGCCTGTCTGTTTTCAACAGACCTGTGAAGCCAAAATACATGAATTCTA
TGGTGAATGTCAGGGGAAGGAAATAGAAACAAAGCAGATGCATGGGTACTGAGTAAGGGAAAAGGAAGCCATATTGGAAG
AGTCTGAAAGAGAGTTCCAGGGCAAATACCTAAAAAAATCCACTAAGAAGGGAGTAAGAAGCTCCGAGAAAAGTGAAGAC
TTTTGGCAGAAGAAATAGCTACTTTCTCTAAAAAGAAAACTGCCTGTGAAATATTCCAGAACCAGTGTTTTCTTGCAACT
GGTAGAAAGAAAAGCAAAGGTCAAATGAATTCCAGC

Alignment

ORF - retro_pcap_358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.93 %
• Parental protein coverage: 59.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TRIHVCLYFITPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTISKSELHKFKIKIMGELVSNGVQIYQF
          ..IHV.LYFI....HSLK.L.L.TMK..D.KVNIIP.I..AD..SK.EL.KF.IK.M..L.SN..QIYQF
Retrocopy SHIHVKLYFIIVADHSLKTLNLLTMKNIDIKVNIIPVIVQADAVSKTELLKFRIKLMSKLISNVIQIYQF

Parental  PTDDEAVAEINAVMNAHLPFAVVGSTEEVKVGNKLVRARQYPWGVVQVENENHCDFVKLREMLIRVNMED
          ..DD...A.IN...NAH.PFAVVGS..EVKV......A.QYPW.VVQVEN.NHCDFVK..EMLI...MED
Retrocopy LRDDDTTAKINSSTNAHVPFAVVGSVDEVKVRMRVTKACQYPWSVVQVENGNHCDFVKSQEMLICTKMED

Parental  LREQTHSRHYELYRRCKLEEMGFQDSDGDSQPFSLQETYEAKRKEFLSELQRKEEEMRQMFVNKVKETEL
          ..EQ.H..H.ELYR.CKL.E.G.........P...Q.T.EAK..EF..E.Q.KE.E..QM....V.E.E.
Retrocopy QQEQMHI*HCELYRFCKLKELGLKHVGSVYKPVCFQQTCEAKIHEFYGECQGKEIETKQMHGY*VREKEA

Parental  ELKEKERELHEKFEHLKR-VHQEEKRKVEEKRRELEEETNAFNRRKAAVEALQSQAFHATSQQPLRKDKD
          .L.E.ERE...K...LK...H.E...K..EK.R.L.EE...F...K.A.E..Q.Q.F.AT......K.K.
Retrocopy ILEESEREFQGKY--LKK<IH*EGSKKLREK*RLLAEEIATFSKKKTACEIFQNQCFLATGR---KKSKG

Parental  KKNRS
          ..N.S
Retrocopy QMNSS

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_358 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Procavia capensis	ENSPCAG00000007178	1 retrocopy	retro_pcap_358 ,
Tupaia belangeri	ENSTBEG00000002323	2 retrocopies	retro_tbel_2252, retro_tbel_3268,