Sequence
atgc intronic sequence ATGC exonic sequence...ctttttctcttccttggcatatgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgtatataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
Basic information
species | Glycine max |
transcript | GLYMA12G06690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 2
ctttttctcttccttggcatatgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgtatataa-agGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
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--gtaactaatcgtcgatg---gtgtctttgatacttcttcttaaattc-ctctatgtttctctacttacccgaagaaacttatgtttttgtatttaatagGAACGAGATAGTTACTGGAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGC
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 2
-----ctttttctcttccttggcat-atgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgtatataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
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aatcttgtcttgaattacccgatatgaaatcatattttagca-atttatcctgtattttttatttgtgctgatattttgagcttgttctgttttct-----tgtagGAAAGGGACAGTTACTGGAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGC
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
ctttttctcttccttggcatatgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgt-atataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
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----------------gtaagt-cttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
upper sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 2
ctttttctcttccttggcatatgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgt-atataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
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----------------gtaagt-cttcccttgttctttttcttgttcttttaatacttgtttttgtttgtttcctcactctttggtctttacgatcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgattctgaatattattatctcttttttctccctttggctcttgtatataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
ttctgat putative branch site (score: 3)
ttatctcttttttctc putative PPT
tgaatattattatctc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttttctcttccttggcatatgcctcattcatacatgctcatattctgattctgaatattattatctcttttttctccctttggctcttgtatataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACATTACCTGTTATTATATTTGAACCAATGACTATGA
- - - ctcttcc
- - - - - - - - - - -tgcctca
- - - - - - - - - - - - - - - - - catgctc
- - - - - - - - - - - - - - - - - - - - - - - - gattctg