RetrogeneDB ID: retro_vpac_585

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_5883:22115..22465(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D1
• Ensembl ID: ENSVPAG00000006944
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 1 [Source:HGNC Symbol;Acc:12474]

Sequence

>retro_vpac_585
GAGCCCCCAGCACAGTGTTCAGCAGGTCCCGCTGGAGGTGATACAGCCCATTGGCTAGCTACAATAATGGGGCCAAACGA
CCGTCCTGATCAGGGTGGAGTATTTTTCTTGACACCTCATTTCCCAACAGGTTACCCCTTCAAACTACCAAAGGGTGCGT
TTACAACAAGAATTTACCGTCCAAATACCAACAGTCATGGCAACAGTTGTCCTGATATTCTGCAGTCATAGTGGTCTCCA
GCACTATTTCAAAAGTACTCTTGTCCATCTGTTCTCTGCGGTGTGACCCCAATCCAGATGATCCTTTAGTGCCTGAGACT
GCTTGGAGGATCTACAAAACAGAGAGAAAA

Alignment

ORF - retro_vpac_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 84.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTRIYHPNINSNASIC
          .PPA.CSAGP.G.D..HW.ATIMGP.D...QGGVFFLT.HFPT.YPFK.PK.AFTTRIY.PN.NS....C
Retrocopy EPPAQCSAGPAGGDTAHWLATIMGPNDRPDQGGVFFLTPHFPTGYPFKLPKGAFTTRIYRPNTNSHGNSC

Parental  LDILKSHWSPAL-TVSVLLSICSLLCDPNPDDPLVPDIA-QIYKSDKE
          .DIL.S.WSPAL....VLLSICSL.CDPNPDDPLVP..A..IYK....
Retrocopy PDILQS*WSPAL<ISKVLLSICSLRCDPNPDDPLVPETAWRIYKTERK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_585 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_585 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos 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 16 parental genes, and 91 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,
Vicugna pacos	ENSVPAG00000007007	3 retrocopies	retro_vpac_108, retro_vpac_315, retro_vpac_425,