RetrogeneDB ID: retro_pcap_260

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_22945:18316..18835(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSPCAG00000009160
• Aliases: None
• Description: transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]

Sequence

>retro_pcap_260
CTGGAGATCCTGTGCTCTGTCAACATCCTTCAGTTCATCTTCATTGCCCTAAGGCTAGACAGGATTATCCACTGGCCGTG
GTTGGTGGTGTTCGTGCCCCTGTGGATCCTCATGTCCTTCCTCTGCCTGGTCGTGCTCTATTACACCGTCTGGTCGCTCC
TCTTCCTGAGGTCCCTGGATGTGGTTGCGGAGCAGCGAAGAACACACGTGACCATGGCAGTGAGCTGGGTAACGATCGTC
GTGCCGCTCCTCACTTTCCAGGTCCTGTTGGCTCACAGAGTGGACGGCCACAATACTTTCTCTTACATATCCATATTTGT
CCCCCTTTGGCTTTCACTAATAACATTGATGGCCACGACATTTAGGCGAAAAGGGGGCAATCATTGGTGGTTTGGTATCC
GCAGAGATTTCTGTCAGTTTCTGCTTGAGATTTTCCCGTTTTTAAGAGAATATGGGAACATTTCATATGACCTACATCAT
GAAGATAGTGAAGATGCTGAAGAAACATCGGTTCCAGAA

Alignment

ORF - retro_pcap_260 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.13 %
• Parental protein coverage: 82.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSILFLRSMDVIAEQRRTHI
          LEILCSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYY.VWS.LFLRS.DV.AEQRRTH.
Retrocopy LEILCSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYTVWSLLFLRSLDVVAEQRRTHV

Parental  TMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQF
          TMA.SW.TIVVPLLTF..LL.H..DGHN.FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIR.DFCQF
Retrocopy TMAVSWVTIVVPLLTFQVLLAHRVDGHNTFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQF

Parental  LLEIFPFLREYGNISYDLHHEDNEETEETPVPE
          LLEIFPFLREYGNISYDLHHED.E..EET.VPE
Retrocopy LLEIFPFLREYGNISYDLHHEDSEDAEETSVPE

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_260 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.

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Bos taurus	ENSBTAG00000006818	1 retrocopy	retro_btau_1,
Canis familiaris	ENSCAFG00000019103	1 retrocopy	retro_cfam_159,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Felis catus	ENSFCAG00000024483	1 retrocopy	retro_fcat_1116,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Procavia capensis	ENSPCAG00000009160	1 retrocopy	retro_pcap_260 ,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,