Sequence
atgc intronic sequence ATGC exonic sequence...aaggttgtagtactctttggaatttagtgttatatggagacttgttttttcattttctagtatcttctatgttttattagccattgacattctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
Basic information
species | Glycine max |
transcript | GLYMA16G23240.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G23240.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g06120.3 (Oryza sativa), 3'ss of exon 6
aaggttgtagtactctttggaatttagtgttatatggagacttgttttttcattttctagtatcttctatgttttattag---ccattgacattcta----tgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
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------gttttatctgaaagaattaccatgcacactatggagcgttcgtatatccta-agagccttttatgttacttaaaactctgtttatgttatgccgctgacagGGAGGTTGCATTGATGATTTCCTATCACATTTGATGTGTTGTTGCTGTGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATG------
upper sequence: GLYMA16G23240.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G17780.3 (Arabidopsis thaliana), 3'ss of exon 7
aaggttgtagtactctttggaatttagtgttatatggagacttgttttttcattttctagtatcttctatgttttattagccattgacattctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
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--------------------------gtacatcaattaaacctctactttcttaaggtcgtgatgctaaggtttttacggatgtcttgaatttg---cagGGAGGGTGCATTGACGACTTTTTGTCACATCTAATGTGTTGTTGTTGTGCCCTTGTCCAAGAACTGAGAGAAGTCGAGATTCATCGAGCTTCTTACGGTA
upper sequence: GLYMA16G23240.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G17780.1 (Arabidopsis thaliana), 3'ss of exon 7
aaggttgtagtactctttggaatttagtgttatatggagacttgttttttcattttctagtatcttctatgttttattagccattgacattctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
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--------------------------gtacatcaattaaacctctactttcttaaggtcgtgatgctaaggtttttacggatgtcttgaatttg---cagGGAGGGTGCATTGACGACTTTTTGTCACATCTAATGTGTTGTTGTTGTGCCCTTGTCCAAGAACTGAGAGAAGTCGAGATTCATCGAGCTTCTTACG---
upper sequence: GLYMA16G23240.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G35920.3 (Arabidopsis thaliana), 3'ss of exon 7
aaggtt--gtagtactctttggaatttagtgttatatggagacttgttttttcattttctagtatcttctatgttttattagccattgacattctatgcc--agGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
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aaaattcagtagtaactatcatggttgagattgaaatgg----ctatgtttatgccactcaatgtagagtcggaatgaatgcttaatgttttctgatttcgcagGGAGGATTCATTGACGATTTTCTATCTCATGTAATGTGTTGTTGCTGTGCCCTTGTACAAGAACTGAGAGAAGTTGAGATTCGTGGGGCATATG------
upper sequence: GLYMA16G23240.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0349g00020.t01 (Vitis vinifera), 3'ss of exon 5
aaggttgtagtactctttggaatttagtgtta-tatggagacttgttttttcattttctagtatcttctatgttttattagccattgaca--ttctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
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---tttgagattctcccacaatctaatcattaacaggtagctttagtgtcgcatgtttaatttccttgaatattttgcttcttattatccctttctttgacagGGAGGCTTGTTTGATGATTTCCTCTCACATCTGATGTGTTGCTGCTGTGCCCTTGTCCAAGAATGGCGAGAAGTGGAGATCCGTGGGGTTTATG------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttcattttctagtatcttctatgttttattagccattgacattctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
cattgac putative branch site (score: 3)
ttctatgttttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggttgtagtactctttggaatttagtgttatatggagacttgttttttcattttctagtatcttctatgttttattagccattgacattctatgccagGGGGGCTTTATTGATGATTTTCTTTCTCATTTGATGTGTTGTTGCTGTGCCCTTGTGCAAGAAAGGAGAGAAGTGGAGATCCGTGGTGTTGAAGGTATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- ggttgta
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