Sequence
atgc intronic sequence ATGC exonic sequence...ctatcctttttcttgatattattgttgttttaatatgtagaagttagacagaataaattttctgaattcatggatttaacatgtatattgcactttgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
Basic information
species | Glycine max |
transcript | GLYMA02G43540.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 6
--ctatcctttttcttgatat-tattgttgttttaatatgtagaagttagacagaataaattttctgaattcatggatttaacatgtatattgcactt-tgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
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gcataattttcatttccatgtctatctgtaatctcatatgttt---ttcagtcgcctaccttacatgagaatagggaatca-cattgatatttcttaaatgcagTATCGAATTTGACCGTGATGATGAGCTATTTGCTACTGCTGGAGTCTCAAAGCGCATCAAAGTCTTCGAGTTTTCTACA
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 6
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 6
-ctatcctttttcttgatattattgttgttttaatatgta-gaagttagacagaataaattttctgaattcatggatttaacatgtatattgcactttgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
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gtttacatgctttatgctttgcctggacctctagtttacctgtaatttgat-gtaccatcttactgattttgctgatgaagagggtgctgttc-cttttcagCATAGAGTTTGATCGTGATGATGAGCTGTTTGCCACTGCTGGTGTTTCTAGATGTATAAAGGTTTTTGACTTCTCTTCG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 6
ctatcctttttcttgatattattgttgttttaatatgtagaagttagacagaataaattttctgaattcatggatttaacatgtatattgcact-ttgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
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acaccatctaagttgtttgtatgtgtgtgtgtgtgttt-gttatctggtattgtgtgattattaaattactgaacttgtcattgctcatgccttatttcagCATAGAATTTGACTGTGATGATGAGTTGTTTGCTACTGCTGGAGTTTCAAGGCGCATAAAGGTTTTCGACTTCTCTTCG
upper sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 6
ctatcctttttcttgatat-tattgttgttttaatatgtagaagttagacagaataaattttctgaattcatggatttaacatgtatattgcactt-tgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
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-gttcatttatatccacgtgtgcgattagtttaccttct-gatttgtaacttgttgaaaattcctcatctgtaaactgacagtggcagtactgcttgtgcagCATTGAGTTTGATAGGGATGATCAGTTGTTTGCAACAGCTGGAGTTTCAAGGCGGATTAAAGTTTTTGAATTTGCAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacagaataaattttctgaattcatggatttaacatgtatattgcactttgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
atttaac putative branch site (score: 3)
aataaattttctgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatcctttttcttgatattattgttgttttaatatgtagaagttagacagaataaattttctgaattcatggatttaacatgtatattgcactttgcagCATAGAGTTTGACCGCGATGATGATTTGTTTGCTACTGCTGGAGTTTCGCGGCGCATCAAAGTTTTTGACTTTTCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - -tatgtag
- - - - - - - - - - - - - - - - - - - - - - - - -agaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat