RetrogeneDB ID: retro_pcap_219

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_17859:17548..17971(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPS2
• Ensembl ID: ENSPCAG00000001197
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase 2 [Source:HGNC Symbol;Acc:9465]

Sequence

>retro_pcap_219
GTAACCTCCATTGCTGACAGCTTGAATGTGGACTTCGCCTTGATTCACAAAGAACGGAAGAAAGCCAATGAAGTGGACCG
TATGGTGCTAGTTGGCGATGTGAAAGATAGAGTGGCTATCCTTGTTGATGACATAGCTGACACTTGTGGTACCATCAGCC
ACGCAGCTGACAAACTTCTCGCAGCTGGAGCCACAACAGTTTATGCGATCTTGACCCATGGAATCTTTTCTGGCCCAGCC
ATGTACTGCATCGACAACGCAGGCTTTGAGGCCGTCGTAGTCACCAACACCATACCTCAGGAGGATAAGAGGAAGCATTG
CTCCAAAATACAGGTGATTGACATCTCCATGATTCTTGCAGAAGCTATCCGAAGAACTCACAATGGGGAATCTGTTTCCT
ACCTGTTCAGCCATGTCCCTTTA

Alignment

ORF - retro_pcap_219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.49 %
• Parental protein coverage: 50.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VTSIADRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATKVYAI
          VTSIAD.LNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDD.ADTCGTI.HAADKLL.AGAT.VYAI
Retrocopy VTSIADSLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDIADTCGTISHAADKLLAAGATTVYAI

Parental  LTHGIFSGPAISRINNAAFEAVVVTNTIPQEDKMKHCAKIQVIDISMILAEAIRRTHNGESVSYLFSHVP
          LTHGIFSGPA...I.NA.FEAVVVTNTIPQEDK.KHC.KIQVIDISMILAEAIRRTHNGESVSYLFSHVP
Retrocopy LTHGIFSGPAMYCIDNAGFEAVVVTNTIPQEDKRKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVP

Parental  L
          L
Retrocopy L

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_219 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011662	2 retrocopies	retro_cfam_1037, retro_cfam_1433,
Callithrix jacchus	ENSCJAG00000003885	1 retrocopy	retro_cjac_364,
Echinops telfairi	ENSETEG00000005166	2 retrocopies	retro_etel_1613, retro_etel_669,
Felis catus	ENSFCAG00000026323	1 retrocopy	retro_fcat_527,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323, retro_mdom_1359, retro_mdom_258, retro_mdom_834,
Otolemur garnettii	ENSOGAG00000016087	1 retrocopy	retro_ogar_1440,
Procavia capensis	ENSPCAG00000001197	2 retrocopies	retro_pcap_219 , retro_pcap_292,
Pongo abelii	ENSPPYG00000020125	1 retrocopy	retro_pabe_3431,
Pteropus vampyrus	ENSPVAG00000009452	1 retrocopy	retro_pvam_1224,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,
Ictidomys tridecemlineatus	ENSSTOG00000006056	1 retrocopy	retro_itri_1668,
Tupaia belangeri	ENSTBEG00000009917	1 retrocopy	retro_tbel_1245,
Tursiops truncatus	ENSTTRG00000003226	1 retrocopy	retro_ttru_1494,