Sequence
atgc intronic sequence ATGC exonic sequencegtgagttaattcccctatgtctgccttttaatggcacactggtcatcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
Basic information
species | Glycine max |
transcript | GLYMA06G13330.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgagttaattcccctatgtctgccttttaatggcacactggtcatcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
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gtgagttgaaagcgatatatc--cctt---gtggca-----gtcttaacat-gtgtgcatagagttctaaaactttattgttttaaatttgt---tgcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 21
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgagttaattcccctatgtctgccttttaatggcacactggtcatcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
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gtgagttgaa-----aaagtttccattttatcttcaca--aattgtc-tcttctctctctatctctcttaacc--aaaagaaggatttatgt---tgcagCTTTTCAAGATCAGTGAAGAAGTAGTGGTTGATGCTACAGATAAAGGGAATATAGCTCGGCTCATCAATCATTCG
upper sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 21
gtgagttaattcccctatgtctgccttttaatggcac----actggtcatcatattatttatgtcatgttatcaacctaaaatgcccta-------------ctcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
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gtgagaatctttctctttctttgtgttctaaaaagaccaccaaaaacaaccaaaacttttacatttcctcatctttcttgagagcattaaaataaattgatattgttgtgtttgcagCTCTTTAAGATCAGTGAAGAAGTGGTAGTCGATGCTACAGATAAAGGAAACATTGCCCGCCTAATCAACCACTCGMapped 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|16105061|gb|BI892801.1|BI892801EST: TTGCAGATTTGAGGGAGGCACGCTATAGATTAGAAGGGAAAGACTGCTAC CTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAAT
genomic: TTGCAGATTTGAGGGAGGCACGCTATAGATTAGAAGGGAAAGACTGCTACgtgagttaat ... gtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAAT
EST:
gi|207832561|gb|GD804847.1|GD804847EST: TTGCAGATTTGAGGGAGGCACGCTATAGATTAGAAGGGAAAGACTGCTAC CTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAAT
genomic: TTGCAGATTTGAGGGAGGCACGCTATAGATTAGAAGGGAAAGACTGCTACgtgagttaat ... gtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
acctaaa putative branch site (score: 3)
ccctactcttgtcttt putative PPT
ttatttatgt 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
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gtgagttaattcccctatgtctgccttttaatggcacactggtcatcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
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