RetrogeneDB ID: retro_pcap_8

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_11470:828..1380(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000000485
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSPCAG00000010977
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_pcap_8
ATGAGAGAGTACAAAGTGGTGGTGCTGGGCTCGGGCGGCGTGGGCAAGTCCGCGCTCACCGTGCAGTTCGTGACCGGCTC
CTTCATCGAGAAGTACGACCCCACCATCGAGGACTTCTACCGCAAGGAGATCGAGGTGGACTCGTCGCCGTCGGTGCTGG
AGATCCTGGACACGGCGGGCACGGAGCAGTTCGCGTCCATGCGGGACCTGTACATCAAGAACGGCCAGGGCTTCATCCTC
GTCTACAGCCTGGTCAACCAGCAGAGCTTCCAGGACATCAAGCCCATGCGGGACCAGATCATCCGCGTGAAGCGGTACGA
GCGCGTGCCCATGATCCTGGTGGGCAACAAGGTGGACCTGGAGGGCGAGCGGGAGGTCTCGTACGGCGAGGGCAAGGCCC
TGGCCGAGGAGTGGAGCTGCCCCTTCATGGAGACGTCGGCCAAAAACAAAGCCTCGGTGGACGAGCTGTTCGCCGAGATC
GTGCGGCAGATGAACTACGCGGCGCAGCCCAACGGCGACGAGGGCTGCTGCTCGGCCTGCGTGATCCTCTGA

Alignment

ORF - retro_pcap_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
          MREYK.VVLGSGGVGKSALTVQFV.G.F.EKYDPTIED.YRK..EVD.....LEILDTAGTEQF..MRDL
Retrocopy MREYKVVVLGSGGVGKSALTVQFVTGSFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMRDL

Parental  YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNN
          Y.KNGQGF.LVYS...Q..F.D....R.QI.RVK....VPMILVGNK.DLE.ER.V....G..LA..W..
Retrocopy YIKNGQGFILVYSLVNQQSFQDIKPMRDQIIRVKRYERVPMILVGNKVDLEGEREVSYGEGKALAEEW-S

Parental  CAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          C.F.E.SAK.K..V.E.F...VRQ.N......G.....S.C..L
Retrocopy CPFMETSAKNKASVDELFAEIVRQMNYAAQPNGDEGCCSACVIL

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_8 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 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dipodomys ordii	ENSDORG00000001086	1 retrocopy	retro_dord_521,
Echinops telfairi	ENSETEG00000000242	1 retrocopy	retro_etel_11,
Homo sapiens	ENSG00000127314	2 retrocopies	retro_hsap_3338, retro_hsap_4234,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Myotis lucifugus	ENSMLUG00000016606	2 retrocopies	retro_mluc_1126, retro_mluc_2211,
Monodelphis domestica	ENSMODG00000007323	5 retrocopies	retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Procavia capensis	ENSPCAG00000010977	1 retrocopy	retro_pcap_8 ,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Sus scrofa	ENSSSCG00000021148	1 retrocopy	retro_sscr_1125,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tursiops truncatus	ENSTTRG00000015712	2 retrocopies	retro_ttru_1105, retro_ttru_134,
Vicugna pacos	ENSVPAG00000000931	2 retrocopies	retro_vpac_283, retro_vpac_408,