Sequence
atgc intronic sequence ATGC exonic sequence...ttgtttccaatcctcttagcttattaactttgtacaccgtaagtttttattatataaatttcacactctaaacaagatatttctgctgtgtaattctcagAATTTGCTTACATGAGGAAAGTAACCACTAAAGCGGATGTGTTCAGCTTTGGTATCATAGTAATGGAGTTTCTAACAAAAAGAAGGCCAACAGGGCTCTC
Basic information
species | Glycine max |
transcript | GLYMA05G25830.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G25830.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G46330.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgtttccaatcctcttagcttattaactttgtacaccgtaagtttttattatataaatttcacactctaaacaagatatttctgctgtgtaattctcagAATTTGCTTACATGAGGAAAGTAACCACTAAAGCGGATGTGTTCAGCTTTGGTATCATAGTAATGGAGTTTCTAACAAAAAGAAGGCCAACAGGGCTCTC
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----gtaaattactcacaacac-ttaattttcaaaaccctaa----ttatgccatcgactt---acttgaaata---cactcttatt-tttcatgaacagAGTTTGCTTATATGAGGAAAGTGACAACAAAAGCCGATGTATTCAGCTTCGGGATCATAATGATGGAGCTGATGACGAAACAGAGACCAACTTCGTTGAA
upper sequence: GLYMA05G25830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0003g02910.t01 (Vitis vinifera), 3'ss of exon 3
--------------ttgtttccaatcctcttagcttattaactttgtacaccgtaagtttttattatataaatttcacactctaaacaagatatttctgctgtgtaattctcagAATTTGCTTACATGAGGAAAGTAACCACTAAAGCGGATGTGTTCAGCTTTGGTATCATAGTAATGGAGTTTCTAACAAAAAGAAGGCCAACAGGGCTCTC
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gtaaccagttcattatctttccaattgcagaagtt--tcagtttcatcctgtgactacttttgt-gtttggtctttacacta-atgaaagacgtttatgctttga-----tcagAGTTCGCATACATGAGGGAGCTCACAACCAAAGTCGATGTGTTCAGCTTTGGGATCATAGTAATGGAGTTCCTAACAAAAAGAAGGCCAACAGGACTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattatataaatttcacactctaaacaagatatttctgctgtgtaattctcagAATTTGCTTACATGAGGAAAGTAACCACTAAAGCGGATGTGTTCAGCTTTGGTATCATAGTAATGGAGTTTCTAACAAAAAGAAGGCCAACAGGGCTCTC
ctctaaa putative branch site (score: 3)
ttctc putative PPT
tatataaatttcaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtttccaatcctcttagcttattaactttgtacaccgtaagtttttattatataaatttcacactctaaacaagatatttctgctgtgtaattctcagAATTTGCTTACATGAGGAAAGTAACCACTAAAGCGGATGTGTTCAGCTTTGGTATCATAGTAATGGAGTTTCTAACAAAAAGAAGGCCAACAGGGCTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - ccaatcc
- - - - - - - - - - - - - - - tgtacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctgt