Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
Basic information
species | Glycine max |
transcript | GLYMA03G03120.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 7
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaat--tctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
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----------------------------------------------------------------------------------------agatttagaaaattggcttgattcttttttcttatttagtttctaggtaatgggcacttatatatcttgcaca---taatcct----taaattcattctt---atgttagGGTTGTTGAAATGCAAGAGATCCTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCAGGTGCTATGGCGACAATAGCAAACCAGCGTAGA
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 3
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttag-atggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagt-ttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
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-------------------------------------gtacatctcattcttcaatttttgctttaatataaaattgtcaatgaatatattttccaaataa-aatttattttatt-----ttctattaggtatatatcatggtattcacaaatttacattattgca--tcaattttgtttttggactatacat--cagGGTTGTTGAAATGCAAGAGATCTTAGATCAACAAGTTGCAGAAGAAGCAGCTGAGGCTGAGGGTGCTGGTGCTATGGCGACAATAACAAACCAACGTAGA
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
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---------------------------------------------------------------------------------------------aacacaaagtctcctatccagaagaaaatgagtagactaatttaaag---tgaactagttaactagaactggtactaactttcaatggtttattctatcaaagGGTTGTTGAGATGCAAGAAATTCTAGACCAACAGCTTGCTGAAGAAGCAGCAGAGGCTGAGGGAGAAGGTGCGATGGCATCTGTAGCAAATCCTCGAAGG
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 8
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
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-------------------------------------------------------------------------------------------tgcaatagatca-ctgcatg-ttattatgtttgaccacatggttcagtttactcaacttta-gtttgaacatagtttt-ttttttctttgttttctct-ttgtagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAACTTGCTGAGGAAGCAGCCGAGGCTGAGGGAGGAGGGACCATGGCATCAATTGCAAATCCTCGTAGA
upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 8
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
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----------------------------------------------------------------------gtgcaatagatcactgcatgttatt-atgtttgaccacatggttcag---tttgctca-----------agtttagttt--------gaacatggtttttttttc--tttgttttctct-ttgtagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAACTTGCTGAGGAAGCAGCCGAGGCTGAGGGAGGAGGGACCATGGCATCAATTGCAAATCCTCGTAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
ttctaaa putative branch site (score: 2)
tcttattttccctttg putative PPT
tctttctaaaaaaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgttgatagtcaattgcactttttttttcccagtcagttcattcccttcatcttgttttagatggtaggttggatgattggaaattctagatgataggttggatgattaaaaattctaatcagccggtagaggagtttaatctttctaaaaaaatgtaatcttattttccctttgtttttcatattccagGGTTGTTGAAATGCAAGAAATCCTTGATCAACAGATTGCAGAAGAAGCAGCTGAGGCTGAAGGGGATGGCGCAATGGCATCAGTTGCAAATCCTCGTAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG