RetrogeneDB ID: retro_pcap_190

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_144706:585..1103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK11
• Ensembl ID: ENSPCAG00000008434
• Aliases: None
• Description: serine/threonine kinase 11 [Source:HGNC Symbol;Acc:11389]

Sequence

>retro_pcap_190
GAGATCCGGCTCCTGCAGCGGCTGCAACACCGGAACATTATCCAGCTAGTCGACGTGCTATGCAATAAGGAGAAGCAAAA
GACCTACATGGTGATGGAGTACTGCATATGCGACCTGCAGGAGATGCTGGACAGCGTGCCCGAGAAGAAGTTCCCTGTGT
GCCAGGCCCACGGGTACTTCTGCCAGCTCATCGACGGGCTGGAGTACCTGCACAGCCAAGGCATCGTGCACAAGGACGTC
AAACCCGGGAACTTGCTGCTCAGCACCAGCGGGACACTGAAGATTTGTGACCTGGGCGTGGCCGAGGCCCTGCACCCGTT
TGCCCAGGACGATACATGCCACACCAGCCAAGGCTCGCCAGCGTTCCAGCCCCCGGAGGTCGTGAACAGCCTGCCACCTT
CTCCGGTTTCAAAATAGACATCTGGTCGGCAGGAGTCACGCTCTATAACATCACCACAGGTCTCTACCCTTTTGACGGGG
ACAGTATCTGTGAGCTGTTGCAGAACATCAGAAGGGGA

Alignment

ORF - retro_pcap_190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.91 %
• Parental protein coverage: 51.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EIQLLRRLRHRNVIQLVDVLCNEEKQKTYMVMEYCVCGMQEMLDSVPEKRFPVCQAHGYFCQLIDGLEYL
          EI.LL.RL.HRN.IQLVDVLCN.EKQKTYMVMEYC.C..QEMLDSVPEK.FPVCQAHGYFCQLIDGLEYL
Retrocopy EIRLLQRLQHRNIIQLVDVLCNKEKQKTYMVMEYCICDLQEMLDSVPEKKFPVCQAHGYFCQLIDGLEYL

Parental  HSQGIVHKDIKPGNLLLTTSGTLKISDLGVAEALHPFAEDDTCRTSQGSPAFQPPEIANGLD-TFSGFKV
          HSQGIVHKD.KPGNLLL.TSGTLKI.DLGVAEALHPFA.DDTC.TSQGSPAFQPPE..N.L..TFSGFK.
Retrocopy HSQGIVHKDVKPGNLLLSTSGTLKICDLGVAEALHPFAQDDTCHTSQGSPAFQPPEVVNSLP<TFSGFKI

Parental  DIWSAGVTLYNITTGLYPFEGDNIYKLFENIGKG
          DIWSAGVTLYNITTGLYPF.GD.I..L..NI..G
Retrocopy DIWSAGVTLYNITTGLYPFDGDSICELLQNIRRG

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_190 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000011567	1 retrocopy	retro_lafr_32,
Procavia capensis	ENSPCAG00000008434	1 retrocopy	retro_pcap_190 ,
Sarcophilus harrisii	ENSSHAG00000007173	1 retrocopy	retro_shar_612,