Sequence
atgc intronic sequence ATGC exonic sequencegtagtgtctcgatatggatagaggaaaagctcaggagataaagttggcatctaacatcttttatttgttgatagacacaatccttcttgaattttctgtggtattttctgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG
Basic information
species | Glycine max |
transcript | GLYMA09G28030.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g18010.1 (Oryza sativa), 3'ss of exon 11
gtagtgtctcgatatggatagaggaaaagctcaggagataaagttggcatctaacatcttttatttgttgatagacacaatccttcttgaattttctgtggtattttctgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG------
| | | | ||| || ||||| | || | | ||| ||| | | | ||| |||||| | | | | |||| ||||||| | || | ||||| ||| ||||||| || |||||||| |||||||||| ||||||||||||||| ||||| ||| | ||||| | |
-------------------------------------ttccaatcacgaacta-tattacttattctct--taaaaaatatcacagttgcttctcat----tatattctgactatataattcactggctttttctttgcagaagA---TATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAAATG
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g18010.2 (Oryza sativa), 3'ss of exon 10
gtagtgtctcgatatggatagaggaaaagctcaggagataaagttggcatctaacatcttttatttgttgatagacacaatccttcttgaattttctgtggtattttctgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG---
| | | | | ||| || ||||| | || | | ||| ||| | | | ||| |||||| | | | | |||| ||||||| | || | ||||| ||| ||||||| || |||||||| |||||||||| ||||||||||||||| ||||| ||| | ||||| | |
----------------------------------catttccaatcacgaacta-tattacttattctct--taaaaaatatcacagttgcttctcat----tatattctgactatataattcactggctttttctttgcagAAGA---TATCATACATTGTGAGAGATGCATTGATCAATGTTGGTCCACTGAAAGATTTTTCATATGGTTTAAGAGCCAATGCAGATCCCAATGCAATGGGAA
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G455115_T01 (Zea mays), 3'ss of exon 11
---------gtagtgtctcgatatggatagaggaaaagctcagg---agataaagttggcatctaacatctttt-atttgttgatagacacaatccttct------tgaattttctgtggtattttctgaactagttaaatagttat--------atttttgctgcagAAATCCT--------TCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG---
| | ||| | | || | | | | | | | | ||| | ||| || ||| ||||| || | | | |||| | | || | | | || | | |||| | | | |||| | | ||| | |||| |||| ||||| ||| | |||| || ||||||||| |||||||||| ||||||||||||||| ||| ||||| | || || |||
gtatgaagaacactttct-gttgtgtggtaactatctgtttatggttaccttctattgcgctgtaatatttttccatttgctgtaggtgatatggtttctactgtctaagttcattttaatggttacatgatgagtttgctgctgctcattgctaatttatttcaccaaaactttacagAAGATCTCATTTGTTGTGAGAGATGCTCTGATCAATGTTGGTCCTCTGAAAGATTTTGCATATGGTTTAAGAACTAATTCTGATCCCAACGCAGCAGGCA
upper sequence: GLYMA09G28030.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 11
gtagtgtctcgatatggatagaggaaaagctcaggagataaagttggcatctaacatcttttatt-tgttgatagacacaatccttcttgaattttctgtggtattttctgaactagttaaatagttatattt--ttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG
| || | | || | | |||| | | ||| | ||| || || | || | | | | || | | | | |||||||||| || || ||||||||||| |||||| | |||| ||||| || |||||||||| | ||||| ||||| || |||||||||||||| || || |
----------------------------------------acttttcctttgtgcaacatgtattgtatcaataagagttaggtagcttatgttctcctttccatg----aagtttctcatattttcttttccaataaatgcagAAATCGTTTTCATTTGCAGTGAGAGATTCACTAGTTAATGTTGGCCCAGTGAAAGATTTTGCGTATGGCTTAAGGATTAATGCTGATGCAAACGCCACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaattttctgtggtattttctgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG
tttttgct CT-rich tract
aactagttaaatagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtgtctcgatatggatagaggaaaagctcaggagataaagttggcatctaacatcttttatttgttgatagacacaatccttcttgaattttctgtggtattttctgaactagttaaatagttatatttttgctgcagAAATCCTTCTCGTTTGCAGTGAGGGATTCATTGATTAACGTTGGTCCTTTGAAAGATTTCTCATATGGTTTAAGAATAAATGCTGATGCAAATGCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT