Sequence
atgc intronic sequence ATGC exonic sequence...ttttagcagtcatgagttttaatgaatttggtttatccttgggtgttttggcatcatcatttgattaatacaaatttttctattggttggctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
Basic information
species | Glycine max |
transcript | GLYMA12G28490.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
ttttagcagtcatgagttttaatgaatttggtttatccttgggtgttttggcatcatcatttgattaatacaaatttttctattggttggctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
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---gtacagtcatg----ctaatatattcttttt-tgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------ttttagcagtcatgagttttaatgaatttggttt-atccttgggtgttttggcatcatcatttgattaatacaaatttttctattggttggctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
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gtagtttgtccttctggtctctaataacttatatgtgtaggatttcaatctccgaaaaactgacgttttccttttatgcatgcttccttgtatctta-tgctcttgtggcagATTCTTAATCCAAACCCAGAAGCTATGTCTAAGCTGATCACAGAAAATGCAAGTGAGGAATTTCTCCATTCGCTGAGTAACTATTGTGCCCTTCAG
upper sequence: GLYMA12G28490.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
ttttagcagtcatgagttttaatgaatttggtttatccttgggtgttttggcatcatcattt-gattaatacaaatttttctattggttgg-ctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
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ttctgataaaatattgaactaccactcaccatcagctcttatgt-ttttggtatcagctttttgacttatttgt-tgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggcatcatcatttgattaatacaaatttttctattggttggctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
gattaat putative branch site (score: 3)
ctccctgc putative PPT
atcatttgattaatac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttagcagtcatgagttttaatgaatttggtttatccttgggtgttttggcatcatcatttgattaatacaaatttttctattggttggctccctgcagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAACGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTTCACTTCAG
- - -gcagtca
- - - - - - - - - - - - - - - - - - - - gggtgtt