Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtctttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgtttaattgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
Basic information
species | Glycine max |
transcript | GLYMA15G01980.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g48620.1 (Oryza sativa), 3'ss of exon 4
------------tgtgtctttcttttgaggatgaag-atcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgtttaattgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
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atacaggctaaccacattctttcttggtacctagtgcatctaaaataagattattcttatcgctga----tatgttttata----tttgcatgcttc-aatgttta----tagGTGTATGCCTTGACCAAAGAACGGGATACATTAAGGAGAGAGCAAAATAAAAAAAGTGATGCAGCTGCTCTTTTGAAAGAAAAGGATGAAATTATCAGTC
upper sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G168654_T01 (Zea mays), 3'ss of exon 12
-------tgtgtc-tttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgtttaattgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
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gtcaaaatgtacaactaatttcttttatgcatgtttcatctatgcatcatcttatgcatagggcataacttttacc---ttttttgtgcctt-gatgtat----gtagGTATATGCACTAACCAAAGAGCGTGATACACTAAGGAGAGAACAGAATAAAAAAAGTGATGCAGCTGCCCTTTTGAAAGAAAAGGATGAGATCATCAATC
upper sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G79830.3 (Arabidopsis thaliana), 3'ss of exon 5
tgtgtctttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgtttaa--ttgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
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---------------gtattatatcttttatcattcttctctttcaattctcttcttt--tcattatatatatatatgccttcacagtgcttatctttgtagGTTTATGCTCTCACCAAAGAGCGGGATACACTTAGAAGAGAACAGAACAAGAAAAGTGATGCTGCGGCCCTTTTGAAAGAAAAGGATGAAATAATAAATC
upper sequence: GLYMA15G01980.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0098g00540.t01 (Vitis vinifera), 3'ss of exon 4
-tgtgtctttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgttta-attgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
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ccttgataagatattaattaaaaaactcaaaatttatctttgtttaattgttagg--attcttgttggtcttgtataaatgcatccggtctgtatgtttcagGTATATGCCCTTACTAAGGAAAGGGATACACTACGAAGAGAACATAGCAGAAAAAGTGATGCTGCTGCCCTTTTGAAAGAAAAAGATGAAATAATCAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatactgagctataactgttatgggattttatgtgtttttggtgtttaattgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
attttatgtgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtctttcttttgaggatgaagatcaaatttctcttttctcttaatactgagctataactgttatgggattttatgtgtttttggtgtttaattgcagGTTTATGCTCTCACTAAGGAAAGGGATACACTCCGTCGAGAGCAGAATAAAAAAAGTGATGCAGCTGCTCTCTTGAAAGAAAAGGATGAAATAATTAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG