Sequence
atgc intronic sequence ATGC exonic sequence...ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
Basic information
species | Glycine max |
transcript | GLYMA03G25740.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 6
--ggaaactgaagttacatataggttttgaa-attttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
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ctcatgtccattgctcagcatttatttttcttatttcctattttagatagcataatatttg---ggacattgatttatgtgagctgcttatttccatttacagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAG
upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 6
--ggaaactgaagttacatataggttttgaa-attttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG-------------------
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ctcatgtccattgctcagcatttatttttcttatttcctattttagatagcataatatttg---ggacattgatttatgtgagctgcttatttccatttacagGGGGAGAACACAAAAATGTCGGCCAGTGATCCAAATTCTGCAATATATGTGACAGATAGTGCTAAAGAAATAAAGACAAAGGTTTGCTTTAAGCATTGTA
upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g17770.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------ggaaactgaag--ttacatataggtt--ttgaaattttctctgaaaaaggtctaaattcttatg----tagatgttatctcacatctttataatataaattctt----gcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
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gtatttcttttagggagagcttggatgtaggactgaacattagagctggtgcaatttgacgacttgtaattaacttgctcagaattttttttggttttacttcgaataatcataatttcacgtgcattactttatgtcgattgcttgatttccttttaacagGGGGAGAGCACTAAAATGTCGGCCAGTGACCCAAACTCTGCAATATATGTGACAGATAATTCTAAACAAATAAAGGCAAAG
upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G04600.3 (Arabidopsis thaliana), 3'ss of exon 8
ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattctt-atgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
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------------------------gcaagtagtttcttaagtacactacacattcctgatttaca---caactaattgccttg----gtcactttacgcagGGAGAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G04600.2 (Arabidopsis thaliana), 3'ss of exon 8
ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
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---------------------------gtagtttcttaagtacactacacattcctgatttaca---caactaattgccttg----gtcactttacgcagggagAGAATGGAAAAATGTCTGCTAGTGATCCAAATTCTGCTATCTATGTGACTGATTCCGCAAAGGACATTAAAAACAAG
upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 7
ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttat---aatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
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---cttctttgatgcttggtggtttctacatatggctgcatcattaattttctttttgtgtaaatcatggctcttgtttttccttgaatttgtatatctgcagGGGGAGACAGGAAAAATGTCTGCTAGTGATCCCAATTCTGCAATATACGTGACTGATTCTGGAAAGGACATTAAGAACAAGMapped 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|112361194|gb|EE400179.1|EE400179EST: TTTCCACAAGCCAAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG GGGGAAACAGGAAAAATGTCCGGCAAGTGATTCCAATTCTGCAATATATGT
genomic: TTTCCACAAGCCA-GCCTTGATTGAATCATTATTCTTCCCAGCATTACAGgtatttttat ... attcttgcagGGGGAAACAGGAAAAATGTCTGCCA-GTGATCCCAATTCTGCAATATATGT
EST:
gi|18039483|gb|BM307777.1|BM307777EST: GTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAG GGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTG
genomic: GTTTCCACAAGCCAGCCTTGATTGAATCATTATTCTTCCCAGCATTACAGgtatttttat ... attcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
atctcac putative branch site (score: 3)
ttcttgc putative PPT
ttatctcacatcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaactgaagttacatataggttttgaaattttctctgaaaaaggtctaaattcttatgtagatgttatctcacatctttataatataaattcttgcagGGGGAAACAGGAAAAATGTCTGCCAGTGATCCCAATTCTGCAATATATGTGACCGATTCTGCAAAAGATATAAAGAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacat