RetrogeneDB ID: retro_tsyr_838

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_21321:11850..12283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSTSYG00000000595
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_tsyr_838
ATAGTGTTGAAACAGATTAACAAGGAGCTTAGTGATTTGATCTATGACCCTCTAGCACAGTGTTCTACTGGCCCAGTCAG
GGATGATGTGTTTCACTGGCAAGCCACAATTATGGGATCTCATGACAGTCCATATTAAGTTGGTGTATGCTTTTGACAAT
TCACTTTCTTACCGACTACCACTTTAAACCACCTAAAATTGCATTTACAAGAATTTGTCATCCAAATAGTAACAGTAATG
ACAGCATTTGTCTCAATATTCTCAGATCACGGTGGTCTCCTGCTTTAACTAGTTCTAAAGTTCTTTTATCCATTTGTTTA
CTGCTATGTGATTCAAACCCAGATGATTCCCCAGTGCCAGAGATCGTACAAATCTATAAAACAGAGATTAGTGATACAGA
ATAGTAGAGGAATGGACTCAGAAGTATGCCATG

Alignment

ORF - retro_tsyr_838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVKRIQKELTDLQRDPPAQCSAGPVGDDLFHWQATIMGPNDSPYQGGVFF-LSIHFPTDYPFKPPKVAF
          ...K.I.KEL.DL..DP.AQCS.GPV.DD.FHWQATIMG..DSPY..GV.F.L.IHF.TDY.FKPPK.AF
Retrocopy IVLKQINKELSDLIYDPLAQCSTGPVRDDVFHWQATIMGSHDSPY*VGVCF<LTIHFLTDYHFKPPKIAF

Parental  TTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPEDPLVPEIAHTYA-DREKYNRLAR
          T..I.HPN.NSN.SICL.ILRS.WSPALT.SKVLLSIC.LLCD.NP.D..VPEI...Y...R....R...
Retrocopy T-RICHPNSNSNDSICLNILRSRWSPALTSSKVLLSICLLLCDSNPDDSPVPEIVQIYK<NRD**YRIVE

Parental  EWTQKYAM
          EWTQKYAM
Retrocopy EWTQKYAM

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_838 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838 , retro_tsyr_919,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tarsius syrichta	ENSTSYG00000005459	1 retrocopy	retro_tsyr_1421,
Tarsius syrichta	ENSTSYG00000011229	3 retrocopies	retro_tsyr_1217, retro_tsyr_1430, retro_tsyr_501,