RetrogeneDB ID: retro_pcap_235

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_20170:10901..11356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSPCAG00000005854
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_pcap_235
ATGTCTCTAGTGATCCCCCAGAAGTTCCAGCACATTATGCGAGTACTCATCACTAACATCGATGGGCGGTAGAAAATAGC
CTTTGCCATCACTGCCATTAAGGGTGTGGGGCAAAGATACGCTCCTGTATGTTGAGGAAAGCAGACATCGACCTCCCCAA
AAGGGCAGGAGAGCTGACTGAGGATGAGGTGGAGCATGTGATCACCCTTATGCAGAATCCACGCCAGTATCAGATTCCAG
ATTGGTTCTTGAACAAACAGAAAGATGTGAAGGATGGGAAATGCAGTCAGGTCCTGGCCAATGGTCTAGACAACAAGCTC
CGAGAAGACCTGGAGCGGCCTAAGTAGATTCGTGCCCACAGAGGGCTGCGCCACGTCTGGGGCCTTCGTGTTTGAGGCCA
GCACACCAAGACTACTGGCCATCGTGGCCACACTGTGGGTGTGTCCAAGAAGAAA

Alignment

ORF - retro_pcap_235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHV-VLRKADIDLTKRAGELTEDEVERVIT
          MSLVIP.KFQHI.RVL.TNIDGR.KIAFAITAIKGVG.RYA.V..LRKADIDL.KRAGELTEDEVE.VIT
Retrocopy MSLVIPQKFQHIMRVLITNIDGR*KIAFAITAIKGVGQRYAPV<MLRKADIDLPKRAGELTEDEVEHVIT

Parental  IMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTT
          .MQNPRQY.IPDWFLN.QKDVKDGK.SQVLANGLDNKLREDLER.K.IRAHRGLRH.WGLRV.GQHTKTT
Retrocopy LMQNPRQYQIPDWFLNKQKDVKDGKCSQVLANGLDNKLREDLERPK*IRAHRGLRHVWGLRV*GQHTKTT

Parental  GRRGRTVGVSKKK
          G.RG.TVGVSKKK
Retrocopy GHRGHTVGVSKKK

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_235 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 14 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000950	7 retrocopies	retro_cfam_1311, retro_cfam_1607, retro_cfam_2132, retro_cfam_414, retro_cfam_522, retro_cfam_789, retro_cfam_856,
Dipodomys ordii	ENSDORG00000013825	6 retrocopies	retro_dord_185, retro_dord_326, retro_dord_426, retro_dord_481, retro_dord_50, retro_dord_772,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Mus musculus	ENSMUSG00000008668	2 retrocopies	retro_mmus_57, retro_mmus_66,
Nomascus leucogenys	ENSNLEG00000006840	10 retrocopies	retro_nleu_1074, retro_nleu_1161, retro_nleu_1176, retro_nleu_1466, retro_nleu_219, retro_nleu_2572, retro_nleu_2616, retro_nleu_525, retro_nleu_60, retro_nleu_737,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Procavia capensis	ENSPCAG00000005854	2 retrocopies	retro_pcap_235 , retro_pcap_319,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,