Sequence
atgc intronic sequence ATGC exonic sequence...tgaagccttgtgttagtgtgttcctggagcttcttttttttattttttattttgtttgacttggttgatgatatttttgatactggttggttttgtttagGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
Basic information
species | Glycine max |
transcript | GLYMA17G34690.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------tgaagccttgtgttagtgtgttcctggagcttcttttttttattttttattttgtttgacttggttgatgatatttttgatactggttggttttgtt-tagGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
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gtaaaaatggcttcaaactctataggatttatgtagtgtataccgctttgactattactgataagtgataacaaaagcgggaagaattagaggtaccgagagagcagtaccatattttacatc-ttcaaactattttgctattgattatcgttttctacattgtagGCCTTGCTTGCAAATATGACTGCTATGTATGCTGTTTACCATGGACCAGAAGGCTTAAAATCTATTGCACAACGGGTTCATGGTCTCGCTGGTGTATTTG
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G33010.1 (Arabidopsis thaliana), 3'ss of exon 1
tgaagccttgtgttagtgtgttcctggagcttcttt-tttttattttttattttgtttgacttggttgatgatatttt---tgatactggttggt----------tttgttt------agGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
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-gtaattacttcttagtatctgattactcatttttcacttttcactattagttcgttcagataactagatgatatgttgattcatgttgatgagtacttcatcttttcattttcctgcagGCGTTGCTTGCCAACATGGCTGCCATGTATGCTGTTTACCATGGACCTGCAGGTCTAAAATCTATTGCCCAGCGTGTCCATGGTCTCGCTGGTATATTTT
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 1
tgaagccttgtgttagtgtgttcctggagcttcttttttttattttttattttgtttgacttggttgatgatatttttgatactggt---tggttttgtttagGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
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--ttgccaagcatga-taggagctcaggattcccttccacaatttttgctatttattatgagagacactgctttgtcttaaatggatatcttgttttatgtagGCATTACTTGCAAATATGGCTGCTATGTTTGCTGTTTATCATGGGCCTGAAGGCCTTAAAACCATTGCTCAACGTGTCCATGGTCTTGCTGGGGTATTTG
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 2
-----tgaagccttgtgttagtgtgttcctggagcttcttttttttattttttattttgtttgacttggttgatgatatttttgatactggttggttttgtttagGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
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tattttcagattctttgttttccttgtaaagaaatggaatttcagagttagcttttgtggtatgctt--ttgtttgaagaactgccttttgttgattt---gtagGCATTGCTTGCAAACATGTCTGCTATGTATGCGGTTTATCATGGACCAGAAGGCCTTAAGACAATTGCACAAAGGGTCCATGGTCTAGCAGCAACTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattttgtttgacttggttgatgatatttttgatactggttggttttgtttagGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
ttttgat putative branch site (score: 4)
ttttgttt putative PPT
atgatatttttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaagccttgtgttagtgtgttcctggagcttcttttttttattttttattttgtttgacttggttgatgatatttttgatactggttggttttgtttagGCACTGCTTGCAAACATGGCTGCCATGTATGCTGTGTATCATGGACCCGAAGGCCTGAAGAACATTGCACACCGTGTTCATGGTCTTGCTGGGGCATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - -ccttgtg
- - - - - - - - tgtgttc
- - - - - - - - - - - - - - gcttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggttgg