Sequence
atgc intronic sequence ATGC exonic sequence...cttttagcagtcatgagtcttaatgaattggtttatccttgggtgttttgacatcatcgtttgattaatacaaatttttctattgattggttccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
Basic information
species | Glycine max |
transcript | GLYMA16G00210.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g01470.1 (Oryza sativa), 3'ss of exon 3
cttttagcagtcatgagtcttaatgaattggtttatccttgggtgttttgacatcatcgtttgattaatacaaatttttctattgattggttccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
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----gtacagtcatg----ctaatatattcttttttgaaaggaaattatagtaaaccagacggaaggaaaactcttactccccaaatcctcccttttcagATTCTTAACCCAAATCCAGAAGCAATGTCAAAGATCGTAACTGAAAATTCCAGTGAGGAGTTCTTGTATTCATTGAGTAACTACTGTGCTCTTCAG
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G49810.1 (Arabidopsis thaliana), 3'ss of exon 3
----------cttttagcagtcatgagtcttaatgaattgg--tttatccttgggtgttttgacatcatcgtttgattaatacaaatttttctattgattggttccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
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gtagtttgtccttctggtctctaataacttatatgtgtaggatttcaatctccgaaaaactgacgttttccttttatgcatgcttccttgtatctt-atgctcttgtggcagATTCTTAATCCAAACCCAGAAGCTATGTCTAAGCTGATCACAGAAAATGCAAGTGAGGAATTTCTCCATTCGCTGAGTAACTATTGTGCCCTTCAG
upper sequence: GLYMA16G00210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 3'ss of exon 4
cttttagcag--tcatgagtcttaatgaattggtttatccttgggtgttttgacatcatcgttt-gattaatacaaatttttctattgattggt-tccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
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-ttctgataaaatattgaactaccactcacca-tcagctcttatgt-ttttggtatcagctttttgacttatttgt-tgtttcccctgtttgttctctttgcagATTCTCAACCCAAATCCTGATGCAATGTCTAAGATGATTACAGAAAATGCCAGCGAGGAATTTCTATATTCACTGAGTAATTATTGTGCACTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgacatcatcgtttgattaatacaaatttttctattgattggttccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
tattgat putative branch site (score: 3)
ttccctgt putative PPT
tttgattaatacaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttagcagtcatgagtcttaatgaattggtttatccttgggtgttttgacatcatcgtttgattaatacaaatttttctattgattggttccctgtagATTCTTAATCCAAATCCAGATGCAATGTCTAAGATGATAACAGAAAATGCAAGCGAGGAATTCCTGCATTCATTGAGTAATTATTGTGCACTTCAG
- - - gcagtca
- - - - - - - - - - - - - - - - - - - - gggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - tgacatc