Sequence
atgc intronic sequence ATGC exonic sequencegtttgactctctctctctcatataaattactgctgataatttgatcatcagattcctaaacttttctgcttaagcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
Basic information
species | Glycine max |
transcript | GLYMA02G09080.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 8
----------------------------gtttgactctctctctctcatataaattactgctgataatttgatcatcagattcctaaactttt-----ctgcttaagc-agAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
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gtaataatactacttctgccaggggaaagtagggctggatgatttgtagctttatttttctagagacatccaacaaagttttcttgacattttggattctgttaatgccagAGGCAAGCTGCGCAATGTGTTGGCCGTGTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 3
---------------------------------------gtttgactctctctctctcatataaattactgctgataatttgatcatcagattcc----taaacttt---tctgcttaag--cagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
| ||||| | | |||| | || || | |||| || | || | | | |||| || ||| |||| ||||| ||||| || || ||||| ||||||||||| || || || ||||||||||| |||||||| ||||| ||||| ||
gtaattcattattactttgaggaaaaaataactccttttgattgacacctcttatctcct-tatgttgtcga-gatatttgtaacacaatttctcgaaataaatttgaaatctcattaatgtcagAGGCAAGCGGCCCAATGTGTCGGTCGTGTTATTCGCTCCAAAGCTGATTATGGGATGATGATATTTGCTGACAAGAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgactctctctctctcatataaattactgctgat----aatttgatcatcag---------attcctaaacttttctg--cttaa-gcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
|| ||| ||| | | | || | | | | || | || | | | | | || ||| ||| || |||| ||||| ||||| ||||| ||||| || || || ||||| ||||||||||||||||| |||||||| ||||||||||||||
gtatgattcttattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactctttttggctttaacacagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------gtttgactctctctctctcatataaattactgct--gataatttgatcatcagattcctaaacttttctgcttaagcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
||||| | | | | | | | | |||| ||||| ||| | ||| || | | | | | ||||||| |||||||| || |||||||| || || |||||||||||||| |||||||| ||||||||||| || ||||||||
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttca--ttaatgagaatgt--aatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
--------------------------------------gtttgactctct-ctctctcatataaattactgctgataatttgatcatcagattcctaaacttttctgcttaag-cagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
| | |||| | |||| | |||||| | |||| | || || | | | | | | | ||| | |||||||| ||||||||||| || ||||| ||||| || || ||||||||||||||||||||||| ||||| ||
gtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatg-acattact-ttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ08988 (Selaginella moellendorffii), 3'ss of exon 8
gtttgactctctctctctcatataaattactgctgataatttgatcatcagattcctaaacttttctgcttaagcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
|| || | | | || || | || | || || | ||||||||||||||||| || || || ||||| || || ||||| || ||||| ||||||||||| ||||||||||| ||
---------------------gcaagttct---ttacgttctgttctccg-----cttattcgtttacctgtaccagAGACAAGCTGCTCAATGCGTAGGCCGTGTCATTCGCTCAAAAGCAGATTACGGAATGATGATATTTGCAGACAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaattactgctgataatttgatcatcagattcctaaacttttctgcttaagcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
tcctaaa putative branch site (score: 2)
cttttctgctt CT-rich tract
ataatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgactctctctctctcatataaattactgctgataatttgatcatcagattcctaaacttttctgcttaagcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT