RetrogeneDB ID: retro_pcap_231

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_196670:1179..1574(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMD
• Ensembl ID: ENSPCAG00000004969
• Aliases: None
• Description: monocyte to macrophage differentiation-associated [Source:HGNC Symbol;Acc:7153]

Sequence

>retro_pcap_231
GAGCATTGTTTTCACGTATGTGATAGAATGGCTGTCTATTTCTTTTTTGCTGTTGCTTAGGCTCCGTAGTAAAATCTCTG
TGAACTTGGAAGCCTGGTATGTCATATGCATTGGTTTATTTGTTTTGTGGCAGCAGAAGAAATCATTTATGTGTTTTCTA
CCATGGAAAGTATAAGGTGTCTGATCTCTTCTTCTGCCTCACAATGGAGTTTTCTCCAGCCTTGGTAGTGACACCAAGAA
GAATACTGACGGTCTTCACAAACTCGCCTATGGATCCTTAATTTATAGCTTGAGAGTTAGTCTTCCGGAACGATGGCCTC
ACTCCATTTGCTCATGCCCTCTGGGACCTGTTTGCTTGTACTGTGGCTGCAGCACATGACCACACCATTTGGAAA

Alignment

ORF - retro_pcap_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.76 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EHCFHMCDRMVIYFFIAASYAPWLNLRELGPLASHMRWFIWLMAAGGTIYVF-LYH-EYKVIELFFYLTM
          EHCFH.CDRM..YFF.A...AP..NL.ELG.L..HM.WFI...AA...IYVF..YH..YKV..LFF.LTM
Retrocopy EHCFHVCDRMAVYFFFAVA*AP**NLCELGSLVCHMHWFICFVAAEEIIYVF<FYHGKYKVSDLFFCLTM

Parental  GFSPALVVT-SMNNTDGLHELACGGLIYCLGV-VFFKSDGIIPFAHAIWHLFVATAAAVHYYAIWK
          .FSPALVVT....NTDGLH.LA.G.LIY.L.V.VF...DG..PFAHA.W.LF..T.AA.H...IWK
Retrocopy EFSPALVVT<TKKNTDGLHKLAYGSLIYSLRV>VF-RNDGLTPFAHALWDLFACTVAAAHDHTIWK

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_231 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670, retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070, retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231 ,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,