RetrogeneDB ID: retro_pcap_172

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_13311:35053..35800(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSPCAG00000008531
• Aliases: None
• Description: phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase [Source:HGNC Symbol;Acc:8587]

Sequence

>retro_pcap_172
GAGAGAGCATGGTTGCCCCAGAACTGTACATTGGTTAATATGAAGATTGAATTTGGTGTTGATGTAACCACCAAAGAAAT
TGTTCTTGCTGATGTTATTGATAACGATTCCTGGAGACTCTGGCCATCAGGAGATCGAAGCTAACAGAAAGACAAACAGT
CGTACCGTGACCTCAAAGAAGTAACTCCTAAAGGGCTACAGATGAGAAAGCAAAATTTTGAGTGGGTTGCAGAAAGAGTA
GAGTTGCTTCTGAAATCAGGAAGTCAGTGCAGGGTTGTAGTACTGATGGACTCAACCTCTGATCTTGATCATTGCGAAAA
AATTAAGAAGGCCTGTGGAAATTCTGGCATTCCATGTGAACTCTGGGTAACATCTGCCCATAAGGGACCAGATGAAACTC
TGAGAATTAAAGCTGAGTATGGAGGGGATGGTGTTCCTAATGTATTTGTAGCAGTAGCAGGTAGAAGCAATGGTTTGGGA
CCAGCAATGTCTGGTAATACTGTGTATCCAGTTATCAGCTGTCCTCCTCTCACCCCAGACTAGCGGCCTCAGGATGTGTG
GTCTTCTCTACGACTACCCAGTGGTCTTGGCTGTTCGACTATACTTTCTCCAGAAGGATCAGCTCAGTTTGCTGCTCAGA
TATTTGGATTAAACAATCATTTGGTATGGGCCAAACTGTGAGCAAGCATATTAAATACATGGATTTCCTTGAAGTGGGCT
GATAAGAAAATCAGAGAATGCAGTTTG

Alignment

ORF - retro_pcap_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.57 %
• Parental protein coverage: 55.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKAWLPQNCTLVDMKIEFGVDVTTKEIVLADVIDNDSWRLWPSGDRSQQKDKQSYRDLKEVTPEGLQMVK
          E.AWLPQNCTLV.MKIEFGVDVTTKEIVLADVIDNDSWRLWPSGDRS.QKDKQSYRDLKEVTP.GLQM.K
Retrocopy ERAWLPQNCTLVNMKIEFGVDVTTKEIVLADVIDNDSWRLWPSGDRS*QKDKQSYRDLKEVTPKGLQMRK

Parental  KNFEWVAERVELLLKSESQCRVVVLMGSTSDLGHCEKIKKACGNFGIPCELRVTSAHKGPDETLRIKAEY
          .NFEWVAERVELLLKS.SQCRVVVLM.STSDL.HCEKIKKACGN.GIPCEL.VTSAHKGPDETLRIKAEY
Retrocopy QNFEWVAERVELLLKSGSQCRVVVLMDSTSDLDHCEKIKKACGNSGIPCELWVTSAHKGPDETLRIKAEY

Parental  EGDGVPTVFVAVAGRSNGLGPVMSGNTAYPVISCPPLTPDWGAQDVWSSLRLPSGLGGSTILSPEGSAQF
          .GDGVP.VFVAVAGRSNGLGP.MSGNT.YPVISCPPLTPD...QDVWSSLRLPSGLG.STILSPEGSAQF
Retrocopy GGDGVPNVFVAVAGRSNGLGPAMSGNTVYPVISCPPLTPD*RPQDVWSSLRLPSGLGCSTILSPEGSAQF

Parental  AAQIFGLNNHLVWAKLRASILNTWISLKQADKKIRECSL
          AAQIFGLNNHLVWAKL.ASILNTWISLK.ADKKIRECSL
Retrocopy AAQIFGLNNHLVWAKL*ASILNTWISLKWADKKIRECSL

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_172 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172 ,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170, retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,