RetrogeneDB ID: retro_pcap_454

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_9571:28906..29392(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP3
• Ensembl ID: ENSPCAG00000011316
• Aliases: None
• Description: FK506 binding protein 3, 25kDa [Source:HGNC Symbol;Acc:3719]

Sequence

>retro_pcap_454
TTTCTTCCAGAATATAAGCTATCAGAGAACATCAAAAATGTGGCCGAGAAAGCAAACCAGGACCATTTGGTTACAGCCTC
TAACTATCTTCTGAAACTAAGCATTGCAAAAGTACCTAGAGTATAAATAAGGTATCCGAGCAAATGAAAAATGTTCAGGT
TAATGACAACAAACCCAGAGAAACCAAATCTGAAGAGACTCTGGAAGAAGGTCACCAAAATAAACTCTGTTCTTAAAAAG
GAAGATAAAACCAACTTCCCCCAAAAGGGACATGTTGTCCATTGTTGGTATACAGAAACACCACAGAATGGAACTGCTTT
TGATATTAATATTCAAACAAGTTCAAAGGAGAAGAAAAATGCCAAGCCTTTCAGTTCTAAGGTTGGAACTGGCAAAGTAA
TTGGAGGATGCGATGAAGCACTCCTGACTATGCATAAGGGAGAAAAGACTGGACTAGAAATTGCACTACAAGGGCTTGTG
GGAAGG

Alignment

ORF - retro_pcap_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.66 %
• Parental protein coverage: 96.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FLAEHKLLGNIKNVAKTANKDHLVTAYNHLF-ETKRFKGTESINKVSEQVKNVKVNDDKPKETKSEETLE
          FL.E.KL..NIKNVA..AN.DHLVTA.N.L..ETK..K.T.SINKVSEQ.KNV.VND.KP.ETKSEETLE
Retrocopy FLPEYKLSENIKNVAEKANQDHLVTASNYLL<ETKHCKST*SINKVSEQMKNVQVNDNKPRETKSEETLE

Parental  EG-PPKYTKSVLKKGDKTNFPK-KGDVVHCWYTGTLQDGTVFDTNIQTSSKKKKNAKPLSFKVGIGKVIR
          EG..PK.T...LK...K...PK.KG.VVHCWYT.T.Q.GT.FD.NIQTSSK.KKNAKP.S.KVG.GKVI.
Retrocopy EG<SPK*T-LFLKRKIKPTSPK<KGHVVHCWYTETPQNGTAFDINIQTSSKEKKNAKPFSSKVGTGKVIG

Parental  GWDEALLTMSKGEKARLEIEPEWAYGK
          G.DEALLTM.KGEK..LEI......G.
Retrocopy GCDEALLTMHKGEKTGLEIALQGLVGR

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_454 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 12 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014018	4 retrocopies	retro_cfam_1788, retro_cfam_440, retro_cfam_616, retro_cfam_798,
Choloepus hoffmanni	ENSCHOG00000000189	1 retrocopy	retro_chof_2315,
Equus caballus	ENSECAG00000018299	2 retrocopies	retro_ecab_352, retro_ecab_565,
Echinops telfairi	ENSETEG00000003358	8 retrocopies	retro_etel_1114, retro_etel_1484, retro_etel_1491, retro_etel_1499, retro_etel_1774, retro_etel_2130, retro_etel_2200, retro_etel_997,
Loxodonta africana	ENSLAFG00000003572	2 retrocopies	retro_lafr_357, retro_lafr_76,
Macropus eugenii	ENSMEUG00000004962	1 retrocopy	retro_meug_679,
Monodelphis domestica	ENSMODG00000007352	1 retrocopy	retro_mdom_1554,
Otolemur garnettii	ENSOGAG00000003012	2 retrocopies	retro_ogar_2247, retro_ogar_3472,
Procavia capensis	ENSPCAG00000008816	2 retrocopies	retro_pcap_289, retro_pcap_37,
Procavia capensis	ENSPCAG00000011316	2 retrocopies	retro_pcap_454 , retro_pcap_78,
Tupaia belangeri	ENSTBEG00000006017	13 retrocopies	retro_tbel_1032, retro_tbel_1125, retro_tbel_1696, retro_tbel_1783, retro_tbel_2151, retro_tbel_2569, retro_tbel_3297, retro_tbel_3567, retro_tbel_3807, retro_tbel_4222, retro_tbel_4482, retro_tbel_730, retro_tbel_800,
Tarsius syrichta	ENSTSYG00000002125	2 retrocopies	retro_tsyr_515, retro_tsyr_820,