RetrogeneDB ID: retro_pcap_218

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_17750:27430..28120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EBP
• Ensembl ID: ENSPCAG00000009202
• Aliases: None
• Description: emopamil binding protein (sterol isomerase) [Source:HGNC Symbol;Acc:3133]

Sequence

>retro_pcap_218
ATGACCACCAACGGCAGCCACTTGCACCCGTACTGGCCTCGGCACCTAAGGCTGGACAACTTTGTGCCTAATGACCACCC
CACTTGGCATCTCCTGGATGGCTTGTTCTCTGTCTCTGGGGTCTTAGTCGTGACCACATGGCTGTTGTCAGGTCAAGCTG
CAGTCGTCCCACTGGGGAACTGGAGACGACTGTCCCTGTGCTGGTTTGCAGTGTGTGGGTTCATTCACATGGTGATCAAG
GGGTAGTTCAGCCTCTACCACGAGGACCTCTTTGGAGACCAAGCCTTCTTATCCCAACTCTGGAAAGAATATGCCAACGG
GGATAGCCGATACATTCTGGGTGACAACTTCACAGTATGCTTGGAGACCATCACAGCTTGGATGTGGGGACCACTCAGCC
TGTGAGTGGTGATTGCTTTTCTCCACCAGCAACCCTTCCACTTTGTCCTACAGCTTGTAGTCTCTGTGGGCCAGATCTAT
GGGGATGTATTCTATTTTCTGGCAGAACACTCTGATGGTTTCCAACACAGGGAGCTAGGTCACTCACAGTACTTTAGGTT
TTACTTTGTCTTCATGAATGCCCTGTGGCTGGTGCTGCCCGGAGTCCTGGTCCTCGATTCTGTGAAGCCTCTCACTTGTT
CCCAGAGCATGCTGGATGCAAAGACCTCAAAAGTCAAGAGGAAGCAGAAC

Alignment

ORF - retro_pcap_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTNGSPLHPYWPRHLRLDNFVPNDRPTWHLLAGLFSVSGVLVVTTWLLSGRAAVVPLGNWRRLSLCWFA
          MTTNGS.LHPYWPRHLRLDNFVPND.PTWHLL.GLFSVSGVLVVTTWLLSG.AAVVPLGNWRRLSLCWFA
Retrocopy MTTNGSHLHPYWPRHLRLDNFVPNDHPTWHLLDGLFSVSGVLVVTTWLLSGQAAVVPLGNWRRLSLCWFA

Parental  VCGFIHMVIEGWFSLYHEDLLGDQAFLSQLWKEYAKGDSRYILGDNFTVCMETITAWMWGPLSLWVVIAF
          VCGFIHMVI.G.FSLYHEDL.GDQAFLSQLWKEYA.GDSRYILGDNFTVC.ETITAWMWGPLSL.VVIAF
Retrocopy VCGFIHMVIKG*FSLYHEDLFGDQAFLSQLWKEYANGDSRYILGDNFTVCLETITAWMWGPLSL*VVIAF

Parental  LRRQPFRFVLQLVVSVGQIYGDVLYFLTEHRDGFQHGELGHPQYFWFYFVFMNALWLVLPGVLVLDSVKH
          L..QPF.FVLQLVVSVGQIYGDV.YFL.EH.DGFQH.ELGH.QYF.FYFVFMNALWLVLPGVLVLDSVK.
Retrocopy LHQQPFHFVLQLVVSVGQIYGDVFYFLAEHSDGFQHRELGHSQYFRFYFVFMNALWLVLPGVLVLDSVKP

Parental  LTCAQSMLDAKTSKVKRKQN
          LTC.QSMLDAKTSKVKRKQN
Retrocopy LTCSQSMLDAKTSKVKRKQN

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_218 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009287	1 retrocopy	retro_btau_1337,
Dipodomys ordii	ENSDORG00000013766	1 retrocopy	retro_dord_32,
Otolemur garnettii	ENSOGAG00000016187	3 retrocopies	retro_ogar_1190, retro_ogar_1191, retro_ogar_1942,
Procavia capensis	ENSPCAG00000009202	1 retrocopy	retro_pcap_218 ,