Sequence
atgc intronic sequence ATGC exonic sequence...ggtaagtcttctcccacacttcaaggtttttgttagcattttcaacactcttgctactggttctaattgttacgtggtcaattttgtttgtgaactaaagGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG
Basic information
species | Glycine max |
transcript | GLYMA06G05170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtaagtcttctcc-cacacttcaaggtttt-tgttagcattttcaacactcttgctac--tggttcta-attgttacgtggtcaattttgtttg--tgaactaa----agGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG
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-gtaagtacacacttcaatcttcatggattcatgatttccccctcaaatttctcgggaaaataatgatggattttgacttctttatttttgtttgattaaatctttattagGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
upper sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 4
ggtaagtcttctcccacacttcaaggtttttgttagcattttcaacactcttgctactggttctaattgttacgtggtcaattttgtttgtgaactaaagGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG
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-gtaagccccctttt---ctttttggtcgaaatgaagaaaccatgtatgagtatattctgttcgtgtttatatttaattgattctacccatgtctttcagGGGGGTATGATATGGAAGAGAAAGCTGCAAGAGCTTACGATCTGGCGGCCCTCAAATACTGGGGACCTTCTACTCATATCAACTTCCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cactcttgctactggttctaattgttacgtggtcaattttgtttgtgaactaaagGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG
ttctaat putative branch site (score: 2)
aattttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtaagtcttctcccacacttcaaggtttttgttagcattttcaacactcttgctactggttctaattgttacgtggtcaattttgtttgtgaactaaagGAGGTTATGATATGGAAGAAAAAGCTGCAAGAGCCTATGATCTCGCGGCTCTTAAGTACTGGGGACCTTCAACGCACATAAACTTTTCG
- - - - - ctcccac
- - - - - - - - - cttcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - -actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg