Sequence
atgc intronic sequence ATGC exonic sequence...aatggtcatatggttaaacctttctttactgaaggtgattagtttcaaaatatttatgatgctagctgaactttgacatttttgaaattgccattgacagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
Basic information
species | Glycine max |
transcript | GLYMA20G24470.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24470.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os10g36490.1 (Oryza sativa), 3'ss of exon 9
---aatggtcatatggttaaacctttctttactgaaggtgattagtttcaaaatatttatgatgctagctgaactttgacatttttgaaattgccattg-acagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
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gtaagagatccatttatctagattatctcttgtaatacttttta--tctgaattgtttaccctataaact---cctttgcatgggtgt--tcattattctatagACATGCAGAAAGCTCTGTCAGGAATTGTTCCTGCAATTGAAAAGGCACGCCTTTATCGAGGTAAAGGAGGAGAGATAATGCGTTCTGCTGTTTCCCGATT
upper sequence: GLYMA20G24470.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G60740.1 (Arabidopsis thaliana), 3'ss of exon 10
---------------------------------------------------------------------------------aat---ggtcatatggttaaacctttcttta--ctgaaggtgattagtttcaaaatatttatgatgctagc--tgaactttgacattt---ttgaaattgccattgacagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
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gttagtaccatctattttttcagctttggcttttgtggcacctttgcatatggaaagtcaaaaatatgggcaccatcttggaatctagactttgtaagcggatttttaatcagatgaaaaattaacagagtttgatggttggcatcgttatcccttatatttaaggttcatgttgcactcaatttttacagATAGCCAAAAGCGTATGGCTGGTATTGTTCCTTCCATTGAGAAAGCACGCCTTTACCGTGGAAAAGGTGGAGAAATAATGCGACTGGCTGTCTCACGATT
upper sequence: GLYMA20G24470.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0048g00470.t01 (Vitis vinifera), 3'ss of exon 10
aatggtcatatggttaaacctttctttactgaa-ggtgattagtttcaaaatatttatgatgctagctgaactttgacatttttgaaattgccattgacagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
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tgtgtctctgcttctaactcaaaagtaattggttgataaattgctttcaagcttctaatttgcaaactaactcatgat-cctgagcatatatttcttccagATAAGCAGACAAGGTTTGTTGGTATAGTTACTGCTATTGAGAAAGCACGCCTTTATCGTGGGAAGGGTGGAGAGATAATGCGTGCTGCTGTTTCCCGGTT
upper sequence: GLYMA20G24470.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ25897 (Selaginella moellendorffii), 3'ss of exon 11
aatggtcatatggttaaacctttctttactgaaggtgattagtttcaaaatatttatgatgctagctgaactttgacatttttgaaattgccattgacagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
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-------------------------------------------------gtactttttgtgcaagtttgcagctg-cattgctaatatcatc--taccagAGAAGGAAAAGCTCGTAGCCGGTATGGTACCAGCCATTGAGAAAGCTCGACTATATCGTGGAAAGGGAGGGGAAATCATGCGTGCCGCTGTTTCGAGGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaatatttatgatgctagctgaactttgacatttttgaaattgccattgacagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
ctttgac putative branch site (score: 4)
acatttttgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatggtcatatggttaaacctttctttactgaaggtgattagtttcaaaatatttatgatgctagctgaactttgacatttttgaaattgccattgacagATAAACAGAGAAGTCTTGCTGGCGTTGCTCCTGCTATTGAGAAAGCACGGCTTTATCGTGGAAAGGGAGGAGAGATAATGCGTGCAGCTGTTTCTCGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - -ggtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa