Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcatgttgacatgttttgttatttgctgaaggtatgacaatcagctatgttgagttttgattacttaacgggcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
Basic information
species | Glycine max |
transcript | GLYMA09G33490.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 5
gtatgtcatgttgacatgttttgttatttgctgaaggtatgacaatcagctatgttgagttttgattacttaacgggcacat--gcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
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gtatataagct--ataaacaccattatt-----gaagcttaaaagtt--ctctcttgattcatcac-actgacaagccattttgttagGGTCATGAAAATGCTTCGGCTGAAAACGGACCATGGATCATCACATTGGATGCGCCAAGCTATATTGCTGTTATGCAGCATGCACGGAACAGAGCACTTC
upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 5
---------gtatgtcatgttgacatgttttgttatttgctgaaggtatgacaatcagctatgttgagttttgattacttaacgggcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
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gtatcaatattaactgaaagatatataaagttccatgtttcgttatttttttagtaaggtttgttaatttttgctt-cttgatatgtgacactagGGCCATGAAAATGCAACTGCTGAGAATGGACCATGGATCATTACACTGGATGCTCCTAGTTATCTTCCTGTCATGCAACATGCTAAAAACCGTGCTCTGC
upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G10540.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtcatgttgacatgttttgttatttgctgaaggtatgacaatcagctatgttgagtt-ttgatta--cttaacgggcacatgc--agGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
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gtataatatctgaaagatttataaagtttcatgttgattt-acattgggttt--ttaagttgttgattcgtcttaatatatatgacccaagGGCCATGAAACTGCAACTGCTGACACTGGACCATGGCTCATTACACTCGATGCTCCTAGTTATCTTCCCGTTATGCAACATGCCAAAAACCGAGCTCTGC
upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------gtatgtcatgttgacatgttttgttatttg---ctgaaggtat-gacaatcagct----atgttgagttttgattacttaacgggcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
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gtatttttagctgatttgtagctcaatttttttgcttgttaatccatttccttcctcaagtccagtaatattggcaattctcttctcattttttgcttatgctcatctacaatcac-ttcagGGGCATAAAGATGCTACTGCTGAGAATGGGCCTTGGATAATTACATTGGATGGTCCAAGCTTTCTTTCTGTTATGCAACATGCTCAAAACCGTTCCTTGCMapped 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|254348573|gb|GR852252.1|GR852252EST: GATTACCTGCCACTGCTCTTGGGTTGGCTGCACAGAGTGCAGTATCCAAG GGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGAT
genomic: GATTACCTGCCACTGCTCTTGGGTTGGCTGCACAGAGTGCAGTATCCAAGgtatgtcatg ... gcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGAT
EST:
gi|308098840|gb|HO760681.1|HO760681EST: GATTACCTGCCACTGCTCTTGGGTTGGCTGCACAGAGTGCAGTATCCAAG GGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGAT
genomic: GATTACCTGCCACTGCTCTTGGGTTGGCTGCACAGAGTGCAGTATCCAAGgtatgtcatg ... gcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaggtatgacaatcagctatgttgagttttgattacttaacgggcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
acttaac putative branch site (score: 3)
ttttgattacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcatgttgacatgttttgttatttgctgaaggtatgacaatcagctatgttgagttttgattacttaacgggcacatgcagGGGCATGAAAATGCCACCGCTGAGAATGGGCCATGGATAATTACATTAGATGCTCCTAGTTTTATTGCTGTTATGCAACATGCTCGCAACCGTTCTTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT