RetrogeneDB ID: retro_pcap_117

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: GeneScaffold_7009:22155..22593(+)
• Located in intron of: ENSPCAG00000007556

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D1
• Ensembl ID: ENSPCAG00000006998
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 1 [Source:HGNC Symbol;Acc:12474]

Sequence

>retro_pcap_117
ATGGTGCTGAAACCAATCAATAAGGAATTTAGTGACTTGGCCTGTGACCCTCCAGTACAGTGCTCTGCAAGTCCAGGTAG
GGATGACACGTTTCATTAGCAAGCCACAATTAAGGGACCCAACGACAGCCCACATCAAGGTGGTGTATTCTTTTTGACAA
TTTCTTTTCCTTCAGACTACCTCTTCAAACCACGTAAGCTTGCGTTTACCAGAACTTACCATCCAAATATTAACAGTAAT
GGCAGCCTTTGTCTAGACATTCTAAGAACGCAATGGTCTCCGGCTTTAACTATTTCTGAAGTTCTTTTATTCATTTGTTC
ACTGCAATGGGATCCAAAGCCAGGTGACCCCTTATTGGCAGAGATTGCACAGATAGATAAAACAGGTAGAGATAAGAACA
ACAAAACATTTTAGGAAGGGACACAAAAGTATGTCATG

Alignment

ORF - retro_pcap_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFT
          M.LK.I.KE.SDL..DPP..CSA.P..DD.FH.QATI.GP.DS..QGGVFFLT..FP.DY.FKP.K.AFT
Retrocopy MVLKPINKEFSDLACDPPVQCSASPGRDDTFH*QATIKGPNDSPHQGGVFFLTISFPSDYLFKPRKLAFT

Parental  TKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHARE
          ...YHPNINSNGS.CLDILR.QWSPALT.S.VLL.ICSL..DP.P.DPL...IAQI.K....K.N....E
Retrocopy -RTYHPNINSNGSLCLDILRTQWSPALTISEVLLFICSLQWDPKPGDPLLAEIAQIDKTGRDKNNKTF*E

Parental  WTQKYAM
          .TQKY.M
Retrocopy GTQKYVM

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_117 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 15 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020796	5 retrocopies	retro_btau_1174, retro_btau_1314, retro_btau_1773, retro_btau_1774, retro_btau_752,
Choloepus hoffmanni	ENSCHOG00000001213	21 retrocopies	retro_chof_1091, retro_chof_1169, retro_chof_1465, retro_chof_1675, retro_chof_1731, retro_chof_2071, retro_chof_2089, retro_chof_2098, retro_chof_2101, retro_chof_2190, retro_chof_2266, retro_chof_2364, retro_chof_2481, retro_chof_2485, retro_chof_2514, retro_chof_2637, retro_chof_619, retro_chof_662, retro_chof_683, retro_chof_728, retro_chof_920,
Dasypus novemcinctus	ENSDNOG00000013821	1 retrocopy	retro_dnov_537,
Echinops telfairi	ENSETEG00000002280	2 retrocopies	retro_etel_1363, retro_etel_1600,
Homo sapiens	ENSG00000072401	2 retrocopies	retro_hsap_4723, retro_hsap_4725,
Macropus eugenii	ENSMEUG00000007238	1 retrocopy	retro_meug_1090,
Microcebus murinus	ENSMICG00000010253	1 retrocopy	retro_mmur_586,
Myotis lucifugus	ENSMLUG00000005710	13 retrocopies	retro_mluc_1019, retro_mluc_1597, retro_mluc_1855, retro_mluc_1914, retro_mluc_1971, retro_mluc_2053, retro_mluc_650, retro_mluc_687, retro_mluc_703, retro_mluc_778, retro_mluc_803, retro_mluc_867, retro_mluc_878,
Mus musculus	ENSMUSG00000019927	22 retrocopies	retro_mmus_3405, retro_mmus_3406, retro_mmus_3407, retro_mmus_3409, retro_mmus_3430, retro_mmus_3432, retro_mmus_3434, retro_mmus_3435, retro_mmus_3436, retro_mmus_3563, retro_mmus_3564, retro_mmus_3565, retro_mmus_3566, retro_mmus_3567, retro_mmus_3587, retro_mmus_3589, retro_mmus_3590, retro_mmus_3591, retro_mmus_3592, retro_mmus_3593, retro_mmus_3594, retro_mmus_3595,
Procavia capensis	ENSPCAG00000006998	1 retrocopy	retro_pcap_117 ,
Pteropus vampyrus	ENSPVAG00000007394	2 retrocopies	retro_pvam_1139, retro_pvam_363,
Sarcophilus harrisii	ENSSHAG00000010481	1 retrocopy	retro_shar_714,
Tarsius syrichta	ENSTSYG00000011229	3 retrocopies	retro_tsyr_1217, retro_tsyr_1430, retro_tsyr_501,
Tursiops truncatus	ENSTTRG00000009244	8 retrocopies	retro_ttru_137, retro_ttru_1649, retro_ttru_1670, retro_ttru_1793, retro_ttru_1853, retro_ttru_376, retro_ttru_443, retro_ttru_96,
Vicugna pacos	ENSVPAG00000006944	5 retrocopies	retro_vpac_343, retro_vpac_513, retro_vpac_561, retro_vpac_585, retro_vpac_587,