RetrogeneDB ID: retro_pcap_303

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_29067:8190..8670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSPCAG00000010038
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_pcap_303
GTAGTCCCAAATGAAGTCATACAGCTGGCAAGTCCAGGCACGGATGGAGTTCAGGAGTTTCAGACACTGACCACTACAAA
TATGGGCGATATTCAGCAAGGTACAATTCTCCAGTACACACAGACCCTTGATGGACAGCAAATTCTTGTCCCCAGCAATC
AGGTGCTTGTGCAGACTCTGCCGGGAGGTACTCCGACATACCAGATCTGCCCTGCTCCTTCAGCTACTTCACTGCCAGTG
ACTTCGGTGATGACGCCTCCCGCTGTGACACCTAAATCTCAGTCGACTAAGACAGAAGACCTCCTACAGAAGAGAGAAGC
GAGACTGATGAAAAATAGAGAAGCTGCAAGAGTATGTCGCAGAAAGAAAAAAGAGTATGTGAAAAGCCTGGAAAATCGTG
TTGCCACTCTGGAAAATCAAAATCGAACTCTGCTAGAACAGATACAAACTTTGAAAGATCTTTATTCCCATAAAAATGTT

Alignment

ORF - retro_pcap_303 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 59.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IAPNGALQLASPGTDGVQGLPALTMTNSGSGQQGTTILQYAQTSDGQQILVPSNQVVVQTASGDMQTYQI
          ..PN...QLASPGTDGVQ....LT.TN.G..QQGT.ILQY.QT.DGQQILVPSNQV.VQT..G...TYQI
Retrocopy VVPNEVIQLASPGTDGVQEFQTLTTTNMGDIQQGT-ILQYTQTLDGQQILVPSNQVLVQTLPGGTPTYQI

Parental  RTTPSATSLPQTVVMTSP-VTLTSQTTKTDDPQLKREIRLMKNREAARECRRKKKEYVKCLENRVAVLEN
          ...PSATSLP.T.VMT.P.VT..SQ.TKT.D...KRE.RLMKNREAAR.CRRKKKEYVK.LENRVA.LEN
Retrocopy CPAPSATSLPVTSVMTPPAVTPKSQSTKTEDLLQKREARLMKNREAARVCRRKKKEYVKSLENRVATLEN

Parental  QNKTLIEELKTLKDLYSHKSV
          QN.TL.E...TLKDLYSHK.V
Retrocopy QNRTLLEQIQTLKDLYSHKNV

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_303 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332, retro_eeur_704,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633,
Mus musculus	ENSMUSG00000023027	1 retrocopy	retro_mmus_3609,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383,
Otolemur garnettii	ENSOGAG00000026029	1 retrocopy	retro_ogar_1378,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303 , retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,