RetrogeneDB ID: retro_pcap_136

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_102027:1201..1551(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSPCAG00000006870
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_pcap_136
AGATTCTTCCCACTCGCAGTCGCTGCTGTGTGGAGACCCTCGAGGAGAAGCCACCATCACCATGTCTGACCAAAAGGCAA
AAGGTTCCACCAAGAACTTGGGGAATAAGAAAGAAGGAGAATACATTTAACTCTGAGTCACAGGGCAAGACAGCAGTGGG
CTTCACTTCAAGATAAAAATGAAAACACTTCTCAAGCAATTAAAATAATTATACTATCAAATATACAGAACTCCAAGTAA
TTCATTCAGGTTTCTCTGAAGGTTAAAGAACTACTATGAATCACACTCCAAAAAGAACTGGGAATTAAAGCAAATGATAA
ATGAAATTTCTGAGGGAAAAACAGGGAGGG

Alignment

ORF - retro_pcap_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 82.27 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RFGLPAVAAVRRPP-GEATVTMSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKE
          RF...AVAAV.RP..GEAT.TMSDQ.AK.ST..LG.KKEGEYI.L.V.GQDSS..HFK.KM.T.LK.LK.
Retrocopy RFFPLAVAAVWRPS>GEATITMSDQKAKGSTKNLGNKKEGEYI*L*VTGQDSSGLHFKIKMKTLLKQLK*

Parental  SYCQ-RGVPMNSLRFLFEGQRIADNHT-PKELGMEEEDV-IEVYQEQTGG
          .Y.Q....P.NS.RFL.........H...KELG....D.......E..GG
Retrocopy LYYQIYRTPSNSFRFL*RLKNYYESHS<QKELGIKANDK<MKFLREKQGG

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_136 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 12 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Microcebus murinus	ENSMICG00000008968	5 retrocopies	retro_mmur_1177, retro_mmur_1300, retro_mmur_1493, retro_mmur_1554, retro_mmur_1602,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Macaca mulatta	ENSMMUG00000005240	7 retrocopies	retro_mmul_1108, retro_mmul_2035, retro_mmul_2081, retro_mmul_313, retro_mmul_373, retro_mmul_450, retro_mmul_855,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Procavia capensis	ENSPCAG00000006870	1 retrocopy	retro_pcap_136 ,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,