RetrogeneDB ID: retro_pcap_11

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_225902:3..1071(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPCAG00000010002
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPCAG00000008662
• Aliases: None
• Description: None

Sequence

>retro_pcap_11
AGGTTCACCATGGAACTAGCAAAAAAAGGTTTTATTGGTCCTGGTGTTGATGTGCTTGCCCCAGACATGGGCTCTGGTGA
ACGCGAGATGTCCTGGATTGCTGACACTTATGCCAGCACTTTAGGGTACTATGATATTAATTCACATGCCTGTGTTACAG
GTAAACCCATCAGTCAGGGTGGTGTCCATGGACGTATCTCTGCTACTGGCCATGGTGTTTTTCTTGGTATTGAAAACTTT
ATCAATGAAACTGCTTACATGAACAGTTTAGGTTTGACATCAGGGCTTCAAAATAAAACATTTGTTGTTCAGGGATTTGG
TAATGTGGGCCGTTATACTATGAGATACTTACATTATTCTGGTGCCAAATGTGTTGGTGTTAGTGACTCTCGTGGCAGCA
TATGGAATTCAGATGGTATTGATCCAGAGGAACTGGAGGACTTCAAATTGCAACATGGATCAGTCATGGGTTTCCCCAAG
GCAAAGCCCTATGAAGGAAGCATTTTGGAAGCTGACTGTGACATACTGATTCCAGCTGCCAGTGAGAAGCAGCTGACAAA
GTTTAATGCACACAAAGTCAAAGCCAAGATCATTGCTGAAGGTGCCAATGGGTCTACAACTCCGGAAGCTCATAAGATTT
TTCTGGCAAAGAACGTTTTGGTGATTCCTGATCTCTACTTGAATGCTGGAGGGGTGACAGTGTCTTACTTTGAGTGGCTG
AAGAATATAAATCATGTCAGTTATGGCCGTTTGACCTTCAAATACGAAAGGGATTCTAACTACTATTTGCTCAAGTCTGT
TCAGGAGAGTTTAGAAAGAACATTTGGCAGGCACAGTGGAACTATTCCCGTTGTACCCACAGCAGGATTCCAAGATAGAA
TATCAGGTGCATCTGAGAAAGACATCATATACTCTGGCTTAGCTTACACGATGGAGTATTCTGCCCGGCAAATCATGAGC
ACTGCCAGAAAGTATAACCTGGGAATGGATATGAGAATAGCGGCATATGTCGTTGCCATTGAGAAAATCTTCAGGGTGTA
CAGTGAAGCTGGTTTGACCTTCAAATAG

Alignment

ORF - retro_pcap_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.46 %
• Parental protein coverage: 52.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DINAHACVTGKPISQGGIHGRISATGRGLFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSM
          DIN.HACVTGKPISQGG.HGRISATG.G.F.GIENFINE..YM..LG.T.G...KTFVVQGFGNVG...M
Retrocopy DINSHACVTGKPISQGGVHGRISATGHGVFLGIENFINETAYMNSLGLTSGLQNKTFVVQGFGNVGRYTM

Parental  RYLHRFGAKCVGVAESEGSIWNPDGIDPKELEDFKLQHGSIRGFPKAKPYEGSILEADCDILIPAASEKQ
          RYLH..GAKCVGV..S.GSIWN.DGIDP.ELEDFKLQHGS..GFPKAKPYEGSILEADCDILIPAASEKQ
Retrocopy RYLHYSGAKCVGVSDSRGSIWNSDGIDPEELEDFKLQHGSVMGFPKAKPYEGSILEADCDILIPAASEKQ

Parental  LTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFK
          LTK.NA..VKAKIIAEGANG.TTPEA.KIFL..N..VIPDLYLNAGGVTVSYFEWLKN.NHVSYGRLTFK
Retrocopy LTKFNAHKVKAKIIAEGANGSTTPEAHKIFLAKNVLVIPDLYLNAGGVTVSYFEWLKNINHVSYGRLTFK

Parental  YERDSNYHLLMSVQESLERKFGKHGGTIPVVPTAEFQDRISGASEKDIVHSGLAYTMERSAR
          YERDSNY.LL.SVQESLER.FG.H.GTIPVVPTA.FQDRISGASEKDI..SGLAYTME.SAR
Retrocopy YERDSNYYLLKSVQESLERTFGRHSGTIPVVPTAGFQDRISGASEKDIIYSGLAYTMEYSAR

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_11 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11 ,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,