RetrogeneDB ID: retro_pcap_241

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_206521:370..712(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITGB1BP1
• Ensembl ID: ENSPCAG00000005976
• Aliases: None
• Description: integrin beta 1 binding protein 1 [Source:HGNC Symbol;Acc:23927]

Sequence

>retro_pcap_241
TCTGTAGATTCCAGCTTTGGGGGCTCTCACGATCCAGTATGGTGGCCAGCCTGGATGTGGATTCCACTAAGAGCTCAGGA
CAAAGCAACAACAATTCAGATACCTGTGCCGAATTTCACATAAAATACATTGGTGCCACAGAGAAGCTGAAACTCCCTGA
AGGAAAATGTCTGGAAGGACCACTAGACCTGATCAATTATGTAGATGTTGCCCAGCAAGATGGGAAGTTGCCTTTTGTTC
CTCTGGAAGAAGCATGTATTATGGGTGTTTTATAAGTATGGCATAAAAGTGTCAACATCTGATCAGTATGATGTTTTGCA
CAGAGATGCTCTGTATTTAATC

Alignment

ORF - retro_pcap_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.93 %
• Parental protein coverage: 64.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVDSSLGG-LSRSSTVASLDTDSTKSSGQSNNNSDTCAEFRIKYVGAIEKLKLPEGKSLEGPLDLINYID
          SVDSS.GG.LSRSS.VASLD.DSTKSSGQSNNNSDTCAEF.IKY.GA.EKLKLPEGK.LEGPLDLINY.D
Retrocopy SVDSSFGG<LSRSSMVASLDVDSTKSSGQSNNNSDTCAEFHIKYIGATEKLKLPEGKCLEGPLDLINYVD

Parental  VAQQDGKLPFVPLEEEFIMGV-SKYGIKVSTSDQYDVLHRHALYLI
          VAQQDGKLPFVPLEE..IMGV..KYGIKVSTSDQYDVLHR.ALYLI
Retrocopy VAQQDGKLPFVPLEEACIMGV>YKYGIKVSTSDQYDVLHRDALYLI

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_241 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 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013063	2 retrocopies	retro_btau_1221, retro_btau_1435,
Choloepus hoffmanni	ENSCHOG00000013602	2 retrocopies	retro_chof_1385, retro_chof_432,
Callithrix jacchus	ENSCJAG00000006250	3 retrocopies	retro_cjac_1650, retro_cjac_2776, retro_cjac_393,
Dasypus novemcinctus	ENSDNOG00000008930	3 retrocopies	retro_dnov_1422, retro_dnov_2198, retro_dnov_727,
Homo sapiens	ENSG00000119185	1 retrocopy	retro_hsap_277,
Gorilla gorilla	ENSGGOG00000001754	1 retrocopy	retro_ggor_321,
Macropus eugenii	ENSMEUG00000006761	1 retrocopy	retro_meug_1434,
Microcebus murinus	ENSMICG00000002359	7 retrocopies	retro_mmur_1251, retro_mmur_1342, retro_mmur_1375, retro_mmur_1523, retro_mmur_1539, retro_mmur_244, retro_mmur_442,
Myotis lucifugus	ENSMLUG00000010629	2 retrocopies	retro_mluc_1218, retro_mluc_1752,
Macaca mulatta	ENSMMUG00000018036	1 retrocopy	retro_mmul_563,
Nomascus leucogenys	ENSNLEG00000013322	1 retrocopy	retro_nleu_1488,
Oryctolagus cuniculus	ENSOCUG00000003726	1 retrocopy	retro_ocun_120,
Otolemur garnettii	ENSOGAG00000001679	4 retrocopies	retro_ogar_1235, retro_ogar_1383, retro_ogar_2353, retro_ogar_981,
Procavia capensis	ENSPCAG00000005976	1 retrocopy	retro_pcap_241 ,
Pongo abelii	ENSPPYG00000012667	1 retrocopy	retro_pabe_391,
Pan troglodytes	ENSPTRG00000011637	1 retrocopy	retro_ptro_231,
Sorex araneus	ENSSARG00000009799	1 retrocopy	retro_sara_735,
Tarsius syrichta	ENSTSYG00000014537	1 retrocopy	retro_tsyr_225,
Tursiops truncatus	ENSTTRG00000000859	1 retrocopy	retro_ttru_712,