RetrogeneDB ID: retro_pcap_316

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_3353:16068..16653(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPD1L
• Ensembl ID: ENSPCAG00000016132
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like [Source:HGNC Symbol;Acc:28956]

Sequence

>retro_pcap_316
GGTTCAGCTATTGCAAAAATCATTGGTAATAATGTCAAGCAATTTCAGAAGTTTGCTTCCACAGTCAAGATGTGGGTCTT
TGAAGAAACAGTTAATGGGAGAAAATTGACAGACATCATAAACAACGACCATGAAAATGTCAAATATCTCCCTGGACACA
GGCTGCCAGAAAATGTAGTTGCAATTTCAGATCTCAACGAGGCCGTGCAGGATGCAGACTTGCTGGTGTTTGTCATTCCT
CACCAGTTTATTCACAGAATCTGTAACGAGATCACTGGGAAGGTGTCTAAAAAAGTGCTGGGAATTACCCTTATCAAGGG
GATAGATAAGGACTCCAAAGGGCTGAAACTCATTTCCGACATCATTCGAGAGAAGGTAGGCATTGACGTCAGTGTGCTCA
TGGGAGCCAACACCGCCAACGAGGTGGCTGCAGAGAAGTTCTGTGAGACCACGATTGGCAGCAAAGTAAAGAACAATGGT
CTTCTCTTCAAGGAGCTTCTGCAGACTCCAAATTTTCGGATTACAGTGGTTGATGATGCAGATACAGTTGAAATTTGCGG
TGCTCTGAAGAACATCATTGCTGTG

Alignment

ORF - retro_pcap_316 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.21 %
• Parental protein coverage: 58.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAVAKIIGNNVKKLHKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHKLPENVIAVSNLNEAVQ
          GSA.AKIIGNNVK...KFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGH.LPENV.A.S.LNEAVQ
Retrocopy GSAIAKIIGNNVKQFQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHRLPENVVAISDLNEAVQ

Parental  DADLLVFVIPHQFIHRICDEITGRVSKKALGITLIKGIDEGPDGLKLISDIIREKMSIDISVLMGANIAN
          DADLLVFVIPHQFIHRIC.EITG.VSKK.LGITLIKGID....GLKLISDIIREK..ID.SVLMGAN.AN
Retrocopy DADLLVFVIPHQFIHRICNEITGKVSKKVLGITLIKGIDKDSKGLKLISDIIREKVGIDVSVLMGANTAN

Parental  EVAAEKFCETTIGSKVMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVAV
          EVAAEKFCETTIGSKV..NGLLFKELLQTPNFRITVVDDADTVE.CGALKNI.AV
Retrocopy EVAAEKFCETTIGSKVKNNGLLFKELLQTPNFRITVVDDADTVEICGALKNIIAV

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_316 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316 ,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,