Sequence
atgc intronic sequence ATGC exonic sequence...gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgtcttttgctaactctatcatttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
Basic information
species | Glycine max |
transcript | GLYMA03G03200.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 4
gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgtcttttgctaactctat-catttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
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---------------gttggtttctt-ttgtatctgcaacctttatgt---ttttttcgctgtggattttataatgttggtctaatttatactccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 4
gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgtcttttgctaactctatcatttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
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---------gtaactacaca----atttcttaaccatcaaacatcggttggtc---taaagacctttgatattgatttaccatattgcgtaatc---cagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 4
gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgtcttttgctaactctatcatttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
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--gtatctgcacactttttttagcca-tgaactcattaagcaacgtttgatctcatggcctttggt--gttaattgttttgtggc---atggttt---agGTCACTACTACAATTGGTTATGGTTCTCCCAACAAGGCAAACTCATACAGTGTCCATGGAGCTGCGCTTGGTGAGAAGGAAGTTGAGGCTACCCGAAACA
upper sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 4
--------------gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgt-cttttgctaactctatcattt-cacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
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gtcatttctccaacatgatctttaaggttttggtcaagagagttccaacttaaacttcttttccccctttt--ctgaagttggactttacctctataaacttctctgtttatgcagGTGACAACTACCATTGGTTATGGTTCTCCTAACAAGGCAAACTCATATAGTGTTCATGGGAGTGCATTGGGTGCTAAAGAAGTAGATGCAACAAGGAAGAMapped 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|14990336|gb|BI316009.1|BI316009EST: CTGCCATTAAGGAAGCAAAAGCTGTCAAAGACAAACCCACATTAATCAAG GTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGT
genomic: CTGCCATTAAGGAAGCAAAAGCTGTCAAAGACAAACCCACATTAATCAAGgttagtttac ... catttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcagtttattaagtgtagctggtttgtcttttgctaactctatcatttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
tgctaac putative branch site (score: 1)
ctctatc CT-rich tract
tttattaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgtcttttgctaactctatcatttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
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gagaaac
- - - - - - - - -aggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctaact