RetrogeneDB ID: retro_pcap_249

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_211535:1098..1606(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSPCAG00000001271
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 1 [Source:HGNC Symbol;Acc:9634]

Sequence

>retro_pcap_249
GTGAACTGCCCAGCTCCTGTGGAAGTCACATATAAGAGCATGTGATTTCTTACTACCCACTATTCAACTAATGTGAACTT
AAACAAAGTCACAGAGAAGTGTAAGAAAAACAGAGTTACCACAAAAGTAACAGTAGGTGAAGCAACTTACGACGCTGCTT
TTGTGAAAAAAGAAGGCATCCACATTCTTGATGGGCCTTTTGATGATGGTGCACCACCACTCACCCGAATTGTTGATGCC
TGGTAAGTCTTGTAAAACTTAAGTTCTGTGAAGAACCTGCTTGTTGTATTGCTGTTCATTGTGTTGCAGGTCTTGGGAGA
GCTTCAGGGCTTGGTGTTCTAGCATTAATTGAAGGTGGAATGAAATATGATGATGCAATATGGTTCATAAGACAAAAGTG
GAGTGGACCTTTTAATAGCAAGAAATTTTAAATTTGGGGAAATATCATCCTAAAATGTAGCTGAGCTTCGAAGTGTCCAA
CGGTCATAGAAACAACTGTTGCATTCAA

Alignment

ORF - retro_pcap_249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.77 %
• Parental protein coverage: 98.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNCPAPAAVQCNSTRFLTNHYSTNMNLNKFIE-LKKYGVTTIVRVCEATYDTALVEKEGIHVLDWPFDDG
          VNCPAP..V...S..FLT.HYSTN.NLNK..E..KK..VTT.V.V.EATYD.A.V.KEGIH.LD.PFDDG
Retrocopy VNCPAPVEVTYKSM*FLTTHYSTNVNLNKVTEKCKKNRVTTKVTVGEATYDAAFVKKEGIHILDGPFDDG

Parental  APPSNQIVDDW-LSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFN
          APP...IVD.W..SLVK.KF.EEP.CCIAVHCVAGLGRA..L..LALIEGGMKY.DA..FIRQK..G.FN
Retrocopy APPLTRIVDAW<VSLVKLKFCEEPACCIAVHCVAGLGRASGLGVLALIEGGMKYDDAIWFIRQKWSGPFN

Parental  SK-QLLYLEKYRPKMRLRFKESNGHRNNCCIQ
          SK...L.L.KY.PKM.L.F..SNGHRNNCCIQ
Retrocopy SK<EILNLGKYHPKM*LSFEVSNGHRNNCCIQ

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_249 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 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018507	4 retrocopies	retro_dnov_1850, retro_dnov_278, retro_dnov_692, retro_dnov_996,
Echinops telfairi	ENSETEG00000008183	6 retrocopies	retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Latimeria chalumnae	ENSLACG00000007183	1 retrocopy	retro_lcha_90,
Myotis lucifugus	ENSMLUG00000001162	1 retrocopy	retro_mluc_264,
Macaca mulatta	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Monodelphis domestica	ENSMODG00000018701	5 retrocopies	retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Procavia capensis	ENSPCAG00000001271	8 retrocopies	retro_pcap_183, retro_pcap_249 , retro_pcap_291, retro_pcap_338, retro_pcap_367, retro_pcap_425, retro_pcap_431, retro_pcap_76,
Rattus norvegicus	ENSRNOG00000011771	4 retrocopies	retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus	ENSRNOG00000046370	4 retrocopies	retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri	ENSTBEG00000009956	14 retrocopies	retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tursiops truncatus	ENSTTRG00000004129	6 retrocopies	retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,