RetrogeneDB ID: retro_pcap_173

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_136055:6115..6699(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSPCAG00000005868
• Aliases: None
• Description: general transcription factor IIF, polypeptide 2, 30kDa [Source:HGNC Symbol;Acc:4653]

Sequence

>retro_pcap_173
GTGTCCTTTACTTTGAATGAGGAGCTTGCAGAGATGCAGGATACTGGTGGAAAACCAGCTTCAGTCAGTGCTGCTAGAGA
ACATCCATTCGTCTTGCAAAGTGTTGGAGGACAGACATTAACGGTACTTACGGAGAGCTCATCGGAGAAACTTTCATTGG
AAGGAGTAGTGGTACCAAGAGCTGAATGCCGACTGCTACCGGGGAAAACTACGTGAGATTCAAAAGATTGCACATAGAAG
AATCTTCTAAGCCGGTGAGACTATCACAACAGCTGGACAAAGTTGTAACGACCAATTACAAACCGGTTGCTAATCATCAG
TACAATATTGAATACGAAAGGAAAAAGAAAAATGGAAAGCGAGCTCGAGCTGAGAAACAACAGGTTTTAGACATGCTGTT
TGCCGCTTTTGACAAGCATCAACATTATCATCTTAAGGACTTGGTGGCCATCACAAAACAGCCTGTGGCGTACCTGAAGG
AAATCTTAAAAGAAATTGGTATTCGGAATGTCCGAGGAAGCCACAGAAACACATGGGAGCTGAAGGCAGAATACAGACCT
TATCCAGGGGAAGACAAGAATGAT

Alignment

ORF - retro_pcap_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.71 %
• Parental protein coverage: 80.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSFTLNEDLANIHDIGGKPASVSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRA-CR-PAASE
          VSFTLNE.LA...D.GGKPASVSA.REHPFVLQSVGGQTLTV.TESSS.KLSLEG.VV.RA.CR..A..E
Retrocopy VSFTLNEELAEMQDTGGKPASVSAAREHPFVLQSVGGQTLTVLTESSSEKLSLEGVVVPRAECR<TATGE

Parental  NYMRLKRLQIEESSKPVRLSQQLDKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVIDMLFSAFE
          NY.R.KRL.IEESSKPVRLSQQLDKVVTTNYKPVANHQYNIEYERKKK..GKRARA.KQ.V.DMLF.AF.
Retrocopy NYVRFKRLHIEESSKPVRLSQQLDKVVTTNYKPVANHQYNIEYERKKK-NGKRARAEKQQVLDMLFAAFD

Parental  KHQYYNLKDLVDITKQPVVYLKEILKEIGIQNVKGTHKNTWELKPEYRHYQGEEKSD
          KHQ.Y.LKDLV.ITKQPV.YLKEILKEIGI.NV.G.H.NTWELK.EYR.Y.GE.K.D
Retrocopy KHQHYHLKDLVAITKQPVAYLKEILKEIGIRNVRGSHRNTWELKAEYRPYPGEDKND

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_173 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Bos taurus	ENSBTAG00000034495	2 retrocopies	retro_btau_1753, retro_btau_208,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Callithrix jacchus	ENSCJAG00000019220	2 retrocopies	retro_cjac_1351, retro_cjac_2990,
Felis catus	ENSFCAG00000002105	1 retrocopy	retro_fcat_526,
Homo sapiens	ENSG00000188342	2 retrocopies	retro_hsap_2990, retro_hsap_368,
Gorilla gorilla	ENSGGOG00000006657	2 retrocopies	retro_ggor_2070, retro_ggor_379,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Macaca mulatta	ENSMMUG00000012634	2 retrocopies	retro_mmul_1913, retro_mmul_483,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Otolemur garnettii	ENSOGAG00000012517	1 retrocopy	retro_ogar_2772,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173 , retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pan troglodytes	ENSPTRG00000005840	3 retrocopies	retro_ptro_2022, retro_ptro_288, retro_ptro_2932,
Pteropus vampyrus	ENSPVAG00000014092	1 retrocopy	retro_pvam_1490,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,
Tursiops truncatus	ENSTTRG00000002729	2 retrocopies	retro_ttru_1003, retro_ttru_850,