Sequence
atgc intronic sequence ATGC exonic sequence...atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
Basic information
species | Glycine max |
transcript | GLYMA08G04110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G105494_T02 (Zea mays), 3'ss of exon 4
atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtg----tgatata---tattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
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-------ttagctacacatcatgtaaaagaagatccatttttacagacaaagatacaaaaacgagatcctgacatggctaacctctttctctcttttttggtggcagACTGACACAGCGTCTGTACTCCTTGAAGCCATTGGGTACATCAGATTCCTCCATAGTCAAATTGAG----------------------------------
upper sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G29100.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------------------atgctctttgtttatat-agcatt--acatagaa-gagaagagatgactgagaatatgactgt-agtgtgtgatata---tattttgattttttttttac-----ttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
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gtaaagatcgattccattaacaaatcaaatttattaatgtcgtctaatattcctctatcaaatcaacttttaacattaattgtggagatttttttagtttcattcttgttaatctaaaatctaaatcattcttcatccctttttacccatcttttgcagACTGACACAGCCTCTGTCCTGTCGGAAGCTATTGGATACATTAGATTCCTTCAGAGTCAAATTGAG----------------------------------
upper sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G20100.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
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gtataattactgattagttccctttactaatcacttgtttaagattatctaatctatgaatcaaaattgaattatattagtcactgtttggtt-gattgatccctt-ttatttcagACTGACACAGCCTCTGTCTTGTCGGAGGCTATTGGATACATTAGATTCCTCCACAGTCAAATTGAG----------------------------------
upper sequence: GLYMA08G04110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03560.t01 (Vitis vinifera), 3'ss of exon 4
-------atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
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atggttcccccccccctttttttttttttttttttcagaaataaagaagac-gtgaatatgactttggagggt----tgtggtgtggtttttttct--cttttgcagACTGACACAGCTTCTGTCTTGTTAGAAGCTATTGGTTATATCAGATTCCTCCAGAGTCAAATTGAG----------------------------------Mapped 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|15204015|gb|BI426783.1|BI426783EST: TAGGTGACAGAATTACCGCCCTTCATCAACTCGTTTCCCCATTCGGAAAG ACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTT
genomic: TAGGTGACAGAATTACCGCCCTTCATCAACTCGTTTCCCCATTCGGAAAGgtataaacct ... acttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
ttttgat putative branch site (score: 4)
ttttgatttttttttt CT-rich tract
tgtgtgatatatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgctctttgtttatatagcattacatagaagagaagagatgactgagaatatgactgtagtgtgtgatatatattttgattttttttttacttttgcagACTGACACGGCTTCTGTCTTATTAGAAGCTATTGGGTATATCAGATTCCTTCAGAGTCAAATTGAGGTCATTAATGTTTATTCTCCTCGCTCTGTCGATT
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