RetrogeneDB ID: retro_pcap_301

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_28780:9548..9806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JTB
• Ensembl ID: ENSPCAG00000003210
• Aliases: None
• Description: jumping translocation breakpoint [Source:HGNC Symbol;Acc:6201]

Sequence

>retro_pcap_301
TGGCTGGTGGAAGAAGAGTATGCCTTGTGTTCTAATCTCCACACTAAAACAATCTCTGAGTGCATTTCCACAGGTATGTG
GAGAGAAAATCACATACAGCCCATCTAAGAGGAATGAGTTCAAAAGCTGCTGCTCAGTGGCGATGGAGCAACTTTGTTCT
GGAAATTTGAAGAGACTGTCGTGGGTGTGGCCTTGGTCTTTGCTTGCCTTGTCATCATTCACCAGTGCCTATTGGACAGA
AAGGCTAGAAGCAAACTG

Alignment

ORF - retro_pcap_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.05 %
• Parental protein coverage: 58.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FVVAEECAPCSFFQAKTIPECTSTGY-VEKITCSPSKRKELKSCRSAVMEQ-RLFWKFEGTVVGLALVFA
          ..V.EE.A.CS....KTI.EC.STG...EKIT.SPSKR.E.KSC.S..MEQ..LFWKFE.TVVG.ALVFA
Retrocopy WLVEEEYALCSNLHTKTISECISTGM>GEKITYSPSKRNEFKSCCSVAMEQ<TLFWKFEETVVGVALVFA

Parental  CLVIIRQRLLDRKALEKV
          CLVII.Q.LLDRKA..K.
Retrocopy CLVIIHQCLLDRKARSKL

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_301 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002520	1 retrocopy	retro_chof_1297,
Callithrix jacchus	ENSCJAG00000009973	1 retrocopy	retro_cjac_496,
Dasypus novemcinctus	ENSDNOG00000000740	1 retrocopy	retro_dnov_1095,
Echinops telfairi	ENSETEG00000008256	1 retrocopy	retro_etel_1340,
Felis catus	ENSFCAG00000012590	2 retrocopies	retro_fcat_1025, retro_fcat_1838,
Myotis lucifugus	ENSMLUG00000013299	1 retrocopy	retro_mluc_2225,
Oryctolagus cuniculus	ENSOCUG00000011788	1 retrocopy	retro_ocun_470,
Procavia capensis	ENSPCAG00000003210	1 retrocopy	retro_pcap_301 ,
Pongo abelii	ENSPPYG00000000791	1 retrocopy	retro_pabe_1886,
Sus scrofa	ENSSSCG00000006559	1 retrocopy	retro_sscr_687,
Tupaia belangeri	ENSTBEG00000012646	1 retrocopy	retro_tbel_762,