Sequence
atgc intronic sequence ATGC exonic sequence...tcaaaatgaatcactaactaactcctaactaactaactgaattacaacatacatcaacagatttttcattttataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG
Basic information
species | Glycine max |
transcript | GLYMA11G14170.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G14170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G12080.2 (Arabidopsis thaliana), 3'ss of exon 6
--------tcaaaatgaatcactaactaactcctaactaactaactgaattacaacatacatcaacagatttttcattt-tataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG
||| ||| || | | | | || ||| || | |||| ||||| ||| | || || || ||| | | | | ||| | || || | | | | | | |||||||| | || |||| || ||| ||||| ||||| | |||||||||||||||||||||||||| |||||||
tagcattgacaactatgttcaataggcatcactttacaaaccaaat--attaaaacattttcttacatctgttgcacccatacgattcaatgacttttctagATCATGGAGAAC-ATTGAAGAGGAGGAAGAAGAAAACTACATTCCTGCCATTGCAATTATTGGTCGGCCAAATGTTGGCAAAAGTAGCATTTTAAATGCAC------
upper sequence: GLYMA11G14170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g02070.t01 (Vitis vinifera), 3'ss of exon 7
tcaaaatgaatcacta-actaactcctaactaactaactgaattacaacatacatc---aacagatttttcattttataatttactttttc-tgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG
| ||| | | | | | ||| | | || | || |||| | | || || || | || | |||||| |||||| ||||| | || | ||||||| || |||||| |||||||||| |||||| |||||||||| ||||||||||||| ||||||||||||||||||||| | ||||
-----ttctttcatttcaatcatccataagcatgcccatattttcccctattcatctggattatatacttaggttcttgataaattttttcatgctaatatatagGATCCTGAGAATCTTGATGGAGAAGAAAATTATGTTCCTGCAATTGCAATTGTTGGACGACCAAATGTTGGTAAAAGTAGCATTTTGAATGCATTAGTTG
upper sequence: GLYMA11G14170.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14023 (Selaginella moellendorffii), 3'ss of exon 4
tcaaaatgaatcactaactaactcctaactaactaactgaattacaacatacatcaacagatttttcattttataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG---
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----------------------------------------------gtatagatgatcagtactgaaagacaataactg--tttttctatttaccagGATGAGTTAGAA------GCGAGCGAAGGCGACCGGCCTTTATCTGTGGCAATTATTGGGAGGCCAAATGTTGGCAAGAGCAGCATTTTGAATGCAATAGTCGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatacatcaacagatttttcattttataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG
tgctaaa putative branch site (score: 2)
tttactttttctgct CT-rich tract
atcaacagatttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaaaatgaatcactaactaactcctaactaactaactgaattacaacatacatcaacagatttttcattttataatttactttttctgctaaactatagAAATCTAATAATCTTGTTGAAGAAGAGGATTATGTTCCGGCAATTTCAATTGTTGGTAGACCAAATGTTGGCAAAAGTAGCATTTTGAATGCACTTGTTG
- aaaatgaa
- - - - - -cactaac
- - - - - - - - - - - - - - - - ctaactg
- - - - - - - - - - - - - - - - - - - - - - - - - -catcaac