Sequence
atgc intronic sequence ATGC exonic sequence...attctttctgctggcaaatacttgttggaagagagaaaagcatatatatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA15G02020.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G02020.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17680.1 (Oryza sativa), 3'ss of exon 3
----attctttctgctggcaaatacttgttggaagagagaaaagcatatatatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG
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gcatggaatcattgtaggttaagagataaggtgagatggggttggagatggaaatgatggcgttct-taattagtatgttttgcttgtgctttttct---tcagGTGAGGAAGGAGAAGCTAGGTGATAGAATAACTGCCCTTCACCAGCTTGTCTCCCCATTTGGGAAG
upper sequence: GLYMA15G02020.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 3
attctttctgctggcaaatacttgttggaagagagaaaagcatatatatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG
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ggacagtcatggaatcattgtggggtggcagagtgtgtgagattggcaggggttggaatgatggcaattttagtatcttttgcttgttcttttgctccagGTGAGGAAGGAGAAGCTAGGGGATCGAATAACTGCTCTCCACCAGCTTGTCTCCCCGTTTGGAAAG
upper sequence: GLYMA15G02020.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g04120.t01 (Vitis vinifera), 3'ss of exon 3
-----attctttctgctggcaaatacttgttggaagagagaaaagcatatatatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG
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aaacagtaaagaaaaaagagagaaattctctagaaaacagaaaactagtaattta----acattctttctttttatatatattaatta-atttactctgaaccagGTGAGAAAGGAGAAGCTGGGTGATAGAATAACAGCCCTTCACCAGTTAGTTTCCCCATTTGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG
aattaat putative branch site (score: 3)
aaattcatgtaattaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attctttctgctggcaaatacttgttggaagagagaaaagcatatatatacaagaaattcatgtaattaatgatttccatgtatgaatattgtgaatcagGTGCGGAAGGAGAAGCTAGGTGATAGAATAACAACCCTTCACCAACTAGTTTCCCCGTTTGGAAAG
- - - -ctgctgg
- - - - - - - - - - cttgttg
- - - - - - - - - - - - - - - -agagaaaa
- - - - - - - - - - - - - - - - - - - -gcatata
- - - - - - - - - - - - - - - - - - - - - - - - -acaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtaa