RetrogeneDB ID: retro_pcap_356

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_48264:11303..11822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUCLG1
• Ensembl ID: ENSPCAG00000013405
• Aliases: None
• Description: succinate-CoA ligase, alpha subunit [Source:HGNC Symbol;Acc:11449]

Sequence

>retro_pcap_356
AGCAGTTTGCTCTGGTCATTCTGTATTGTGCAACAGAATGGAATTCAACATTGTCACTATGCGTCTTCCTGGAAAATCTT
TACATCAACAAAAATGTAAGAGTTATTTGCCGGAGTTTCAGCTGGTGAGCGGGGCATCTTTTATAGCCAAAAGGCATTAG
AATGGCACCAAACTTGTTGGAGGAACCACCCTAGTGAAGGGAGGCAGGATCATCTAGACTTAACCTGTGTTAAGACTATG
GAGGAGGTCAAAGAAAGACAGGAGCAGTAACGGTTGCCATTTTTCTCCTATTTCATTTTCTGCTGCTGCAATTAAGGCAG
AATACTACTGCTTGTGTGCATCACTGGAGGTATTCCCCAGCAGGACATGGTGTGGGTTAAGCACGCACTGATGAGCCAGG
GAAAGACAAGGCTGATTGTGCCACACTGCCTTGGGGTCATCAGTCCTGGAGAAGGCAAAACTGTCATCAGGCCTGGCGAT
AGTCACAAGAAATGAAGAGTTGGCATTATATCCACATCT

Alignment

ORF - retro_pcap_356 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.84 %
• Parental protein coverage: 53.41 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SRLLTRYFLVQRNGIRHDSSYTLSRK-NLYINKSTRVICQGFTGKQGTFHSQKALEY-GTKLVGGTT-PG
          S.LL.....VQ.NGI.H...Y..S.K.NLYINK..RVIC..F....G.....K.....GTKLVGGTT.P.
Retrocopy SSLLWSFCIVQQNGIQH-CHYASSWK<NLYINKNVRVICRSFSW*AGHLL*PKGIRM<GTKLVGGTT<PS

Parental  KGGQKHLDLPVFDTVKEAKEA-TGATASVIYV-PPPFAAAAINEAVEAE-IPLVVCITEGIPQQDMVRVK
          .G.Q.HLDL....T..E.KE..TGA....I...P..F.AA....A..AE.I.L.VCIT.GIPQQDMV.VK
Retrocopy EGRQDHLDLTCVKTMEEVKER<TGAVTVAIFL<PISFSAA----AIKAE<ILLLVCITGGIPQQDMVWVK

Parental  HALLRQTKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRVGIVSRS
          HAL..Q.KTRLI.P.C.GVI.PGE.K..I.PG..HKK.RVGI.S.S
Retrocopy HALMSQGKTRLIVPHCLGVISPGEGKTVIRPGDSHKK*RVGIISTS

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_356 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003017	1 retrocopy	retro_cpor_1170,
Myotis lucifugus	ENSMLUG00000012370	1 retrocopy	retro_mluc_1231,
Procavia capensis	ENSPCAG00000013405	1 retrocopy	retro_pcap_356 ,
Pteropus vampyrus	ENSPVAG00000003656	2 retrocopies	retro_pvam_1160, retro_pvam_670,
Drosophila melanogaster	FBgn0004888	1 retrocopy	retro_dmel_47,