Sequence
atgc intronic sequence ATGC exonic sequence...atgcatgcacacagatacccagttcatttgatcaattttgagtttccttgatgattttgatttaaaagaatgagtgactaaatgaatagtctgctttcagACTTGTCTTGTTGGAGCTGGTCCTGATGGAAAACATAAAGCTTTAGAAGCAGTCACAATTGTACTTGATCTACCACCTCCGCAGCCTGGGTCAATGCTTG
Basic information
species | Glycine max |
transcript | GLYMA05G36530.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 3'ss of exon 13
--------------------------------------------------------atgcatgcacacagatacccagttcatttgatcaattt-------tgagtttcctt-------gatga--ttttgatttaaaagaatgagtgactaaatgaatag-------tctgctttcagACTTGTCTTGTTGGAGCTGGTCCTGATGGAAAACATAAAGCTTTAGAAGCAGTCACAATTGTACTTGATCTACCACCTCCGCAGCCTGGGTCAATGCTTG
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gtatatgccttttatcatacattacgattaatgtcatattgaatcaccaaggtttacttcatgaa-agagac-cccaatttctgtggtcagtttgcaaagctgcaactacttctgtttggatgagacttttttttatacgataaaactatgacaataataacatttgttatctttctagACATGCCTTGTTGGAGCAGGACCAGATGGAAAACATACAGCTTTGGAAGCTGTGACAATAGTCCTTGATCTACCACCACCTCAGCCTGGTTCAATGTCTG
upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G07360.2 (Arabidopsis thaliana), 3'ss of exon 16
atgcatgcacacagatacccagttcatttgatcaattttga-gtttccttgatgattttgatttaaaagaatga-gtgactaaatgaatagtctgctttcagACTTGTCTTGTTGGAGCTGGTCCTGATGGAAAACATAAAGCTTTAGAAGCAGTCACAATTGTACTTGATCTACCACCTCCGCAGCCTGGGTCAATGCTTG
| || || | || | || ||||| | | ||| | | ||| | | | | | | | | ||| |||| ||||||||||||||||||||||| || ||||| | |||| | ||||||||||| || ||||| |||||||||||||| || || ||||| ||| ||
--gtatatttgcaaggcttaaattattgtgggatattttactgaatttttgctacctcagatagtattttttaacacaatttatcatctgattgacttctagACATGTCTTGTTGGAGCTGGTCCTGACGGGAAACACACAGCTCTGGAAGCAGTCACGATAGTACTCGATCTACCACCTCCACAACCGGGGTCCATGGCTG
upper sequence: GLYMA05G36530.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 3'ss of exon 16
atgcatgcacacagatacccagttcatttgatcaattttgagtttccttgatgattttgatttaaaagaatgagtgactaa--atgaatagtctgctttcagACTTGTCTTGTTGGAGCTGGTCCTGATGGAAAACATAAAGCTTTAGAAGCAGTCACAATTGTACTTGATCTACCACCTCCGCAGCCTGGGTCAATGCTTG
| | | | | |||| | | ||| ||| | || |||| ||| | ||| | || || | | | |||||||| || ||||| ||||||||||||||||| ||||| | |||| | |||||||||||||| || |||||||||||||| || || ||||| |||||| | |
-tcagtttcttcttgccgtctttatatttaaggtttgttgtctttgccatttgctttt-attgatgagatctttcaagtatttattgacaattccatttcagACGTGCCTTGTCGGAGCTGGTCCTGATGGGAAACACACAGCTCTGGAAGCAGTCACAATAGTTCTTGATCTACCACCACCACAACCTGGTTCAATGTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgatgattttgatttaaaagaatgagtgactaaatgaatagtctgctttcagACTTGTCTTGTTGGAGCTGGTCCTGATGGAAAACATAAAGCTTTAGAAGCAGTCACAATTGTACTTGATCTACCACCTCCGCAGCCTGGGTCAATGCTTG
gactaaa putative branch site (score: 2)
tctgctttc putative PPT
atgattttgatttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcatgcacacagatacccagttcatttgatcaattttgagtttccttgatgattttgatttaaaagaatgagtgactaaatgaatagtctgctttcagACTTGTCTTGTTGGAGCTGGTCCTGATGGAAAACATAAAGCTTTAGAAGCAGTCACAATTGTACTTGATCTACCACCTCCGCAGCCTGGGTCAATGCTTG
- -catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtga