Sequence
atgc intronic sequence ATGC exonic sequence...gattttatgctgaatagagattgtagtaggtcacaagaagagatccaatgaagttatagtcttcaaattatgtttctaatggtttctggtgatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG
Basic information
species | Glycine max |
transcript | GLYMA05G33980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 1
gattttatgctgaatagagattgtagtaggtcacaagaagagatccaatgaagttatagtcttcaaattatgtttctaatggtttctggtgatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG
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-------------gtagattttgtttccaatttt-----gatatcta--gatttgattcattccgagaaaaatcatgaataaaatctagcaatttctcagGGAATACCTAATGCTGAATTCTTCACGGAGTATGGAGAAGCAAATAGATATCAGATTCAAGAAGTAGTTGGCAAAGGAAGCTATGGAGTTGTTGGTTCTG
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 2
gattttatgctgaatagagattgtagtaggtcacaagaagagatccaatgaagttatagtcttcaaattatgtttctaatggtttctggtg---atca--agcagGGTGCACCAGAG----ACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG------
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----------aggataaagtttc-----agttttgtgtttcgtttgattgatcttattgtcttgatccatcattttggtcaattttaagtatgaatcatgaataaaattcttcagGGTGAAACTGAATTCTTCACGGAGTATGGAGAAGCTAACAGGTATCAGATTCAAGAGGTTGTTGGCAAAGGAAGTTATGGTGTTGTGGCTTCTGCTGTTG
upper sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 1
--------gattttatgctgaatagagattgtagtaggtca--caagaagagatccaatgaagttatagtcttcaaattatgttt-ctaatggtttctggtgatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG
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aaaaaaaatattttcttctccatt----ctgtactaattcaaccatttatatacttgattaattgata-------aataatgattgctaagggagaccattttttactcagGGCATGCCAGAAACAGAATTCTTCACAGAATATGGAGAGGCGAGCAGATACCAAGTCCAGGAAGTTGTTGGCAAAGGAAGTTATGGTGTTGTTGGCTCTGMapped 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|193481801|gb|FK446920.1|FK446920EST: TTCCCTCACAAATCCCCTTCAGACCCTCTTCCATGGATCATCACAAAAAG GGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATAT
genomic: TTCCCTCACAAATCCCCTTCAGACCCTCTTCCATGGATCATCACAAAAAGgttcttcttt ... gatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATAT
EST:
gi|192306378|gb|FG996138.1|FG996138EST: TTCCCTCACAAATCCCCTTCAGACCCTCTTCCATGGATCATCACAAAAAG GGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATAT
genomic: TTCCCTCACAAATCCCCTTCAGACCCTCTTCCATGGATCATCACAAAAAGgttcttcttt ... gatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgaagttatagtcttcaaattatgtttctaatggtttctggtgatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG
ttctaat putative branch site (score: 2)
aaattatgtttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattttatgctgaatagagattgtagtaggtcacaagaagagatccaatgaagttatagtcttcaaattatgtttctaatggtttctggtgatcaagcagGGTGCACCAGAGACAGAGTTTTTTACCGAGTATGGAGAGGCAAGTCAATATCAGATCCAAGAGGTTGTTGGAAAAGGAAGTTATGGTGTTGTGGGTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - ccaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttctg