Sequence
atgc intronic sequence ATGC exonic sequence...tcaagtgcttttactttccaatataaaataaaacaatatgattgttttgttttgttattgtgattgtgattgtaacttgcaagtaaagttgtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG
Basic information
species | Glycine max |
transcript | GLYMA03G16660.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G79210.1 (Arabidopsis thaliana), 3'ss of exon 1
---tcaagtgcttttactttccaatataaaataaaacaatatgattgttttgttttgttattgtgattgtgattgtaacttgcaagtaaagttgtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG
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ggtttcttttcatttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagatgacactatttcgcattttttgcagCTTGATTTAGT-TGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 1
------------------tcaagtgcttttactttccaatataaaataaaacaat----atgattgttttgttttgttattgtgattgtgattgtaacttgcaagtaaagttgtga-----ttgcagATT--CTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG
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ttcagtctacttacttgctcagacgtggtttcttttca-tttaagtttgaacattgttgatgaagaacagatttagcttccacgtttctaaatttccagagATGACACTATTTCGCATTTTTTGCAGCTTGATTTAGTTGGTTTTCAATGGGGGACAGTCAGTACTCGTTTTCTCTCACCACCTTCAG
upper sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------tcaagtgctttt--actttccaat-ataaaataaaacaatatgattgttttgttttgttattgtga--ttgtgattgtaacttgcaagtaaa----------------gttgtgattgcagATT---CTTGTGCGGTTTA----TCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG
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gtaagctattctcttcacagcgctagttcttttccgaagattcgtgtcgatctcaaaaatcccattctatcaaattgtttttaagactctaatgatttaaccaaacca-aaacctgaatcgtttgatcccggtgacgttgaaaccctgaattccggggaaattgatcctactcgtttgtgttgttcacagCTTTCGCTAATTTGCTTAAGGAGCTATGGGAGATAGTCAGTACTCGTTTTCTCTCACCACTTTCAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|151411475|gb|EV281286.1|EV281286EST: ACTTTGAGTCACCAGGGCAGCCTCGAAACCTCGTCCA ATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATCCGTTTTCTCTCACC
genomic: ACTTTGAGTCACCAGGGCAGCCTCGAAACCTCGTCCAgtaagtgttt ... gtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACC
EST:
gi|9899371|gb|BE608339.1|BE608339EST: AGTCCCTACTTCCACTTTGAGTCACCAGGGCAGCCTCGAAACCTCGTCCA ATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACC
genomic: AGTCCCTACTTCCACTTTGAGTCACCAGGGCAGCCTCGAAACCTCGTCCAgtaagtgttt ... gtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttttgttattgtgattgtgattgtaacttgcaagtaaagttgtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG
ttgtaac putative branch site (score: 2)
tttgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaagtgcttttactttccaatataaaataaaacaatatgattgttttgttttgttattgtgattgtgattgtaacttgcaagtaaagttgtgattgcagATTCTTGTGCGGTTTATCATGGGGGATAGTCAGTATTCGTTTTCTCTCACCACATTTAG
-caagtgc
- - - - - - -ctttcca
- - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaagt