RetrogeneDB ID: retro_pcap_186

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_143099:255..795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSPCAG00000016432
• Aliases: None
• Description: syndecan binding protein (syntenin) [Source:HGNC Symbol;Acc:10662]

Sequence

>retro_pcap_186
ATGTGTTTGTATCCATCTCTTGAAGACTTGAAAGTACACAAAGCAATTCAGGCTCAAGTGGCCCTTTCTGCAAACCCTGC
CAATCCAGCGATTTTGTGAGAGGCTTCCGCTCCCATCTATCAAGATGGAATTCTACATCCTAAACTGTATCTGGAGCTCT
CCCAATACATGGGTCTGAATCTAAATGAAGAAGAAATACATGCAAATATGGCTGTGGTCCCTGGAACGATAGTGCAGGGG
CTGGTAGCAAGGCCTTTCACTATGAGTTACGTGGTGTCTCCTGTAACTGAGAATGATGTTGGAATTTGAAGAGCAGAAAT
TAAGCAAAGAATTCATGAAGTTATTTTGTGTACGGATCAAGATGGAAAAATTGGCCTCAGGCTTAAATCAATAGATAATG
GTGTGTTTGTTCAGCTAGTTCAGGCTAACTCTCCATTATTTTCGGTTGATCTGAGGTTTGGGGACCAGGTACTCCAGATT
AATGGTGAAAACGGTGCTTGGACAAAGCACACGAAGTACTCAAACCGGTTTTCAGAAAAA

Alignment

ORF - retro_pcap_186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 61.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVIQAQAAFSANPANPAILSEASAPISQDGNLYPKLYPELSQYMGLNLNEEEIHANM
          M.LYPSLEDLKV.K.IQAQ.A.SANPANPAIL.EASAPI.QDG.L.PKLY.ELSQYMGLNLNEEEIHANM
Retrocopy MCLYPSLEDLKVHKAIQAQVALSANPANPAIL*EASAPIYQDGILHPKLYLELSQYMGLNLNEEEIHANM

Parental  AMVPGAPVQGHLVARPSSMNYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGVFVQL
          A.VPG..VQG.LVARP..M.Y.V.PVT.NDVGI.RAEIKQ.I.EVILC.DQDGKIGLRLKSIDNGVFVQL
Retrocopy AVVPGTIVQG-LVARPFTMSYVVSPVTENDVGI*RAEIKQRIHEVILCTDQDGKIGLRLKSIDNGVFVQL

Parental  VQANSPSSLVGLRFGDQ-LQINGECAGWSSDKAHKVLKQAFGEK
          VQANSP...V.LRFGDQ.LQINGE...W.....H......F.EK
Retrocopy VQANSPLFSVDLRFGDQVLQINGENGAWTK---HTKYSNRFSEK

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_186 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 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186 ,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,