Sequence
atgc intronic sequence ATGC exonic sequence...cggttttgaatgtgatgttcaagccaattatgttgttaccttcttgtggttctttgaacaagttcacttgtttacacttacttccacctgactctttaagTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
Basic information
species | Glycine max |
transcript | GLYMA13G20930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 4
-cggttttgaatgtgatgttcaagccaat-tatgttgttaccttcttgtggttctttgaacaagttcacttgtttacacttacttccacctgactcttta-agTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
| | | ||| || |||| | | | || || |||| | ||| | |||| | | ||| | | | | || |||| ||||||| | ||| |||||||| | |||||||||||||| ||||| ||||| |||||||| ||||| ||| ||||| ||
attatggtagctttgaattttaagcaagcgcaaaaagataattttttgt---ttcttgttttcacactggagtttttatatgtttcacctaaaatgtctatagTGCGGAGCAATTGGTGGACATTGGCTGCCAATGGGTTATTCTTGGGCATTCAGAGCGTAGACATGTCATTGGTGAAGATGATCAG
upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G002807_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------------cggtttt---gaatgtgatgttcaagccaattat---gttgttaccttcttgtggttctttgaacaagttcacttgtttacacttacttccacctgactctttaagTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
|||||| | ||| | | | | ||| | || ||| | ||| | || || | | ||| | ||| | || |||| || ||||| ||| | ||||| | ||||||||||||||||| |||||||| |||||| | ||||| ||||||||||||
gttgggtacactggacactgagcacccttttctttgctaactatatacatagagattgcaactatctgtaaagcggttataaaatccagtctgttggttttactggatggactttgtataatagttaacgagggattgggagctttttcttcacttc-tggttttgctaatagagttttatctttcccttaaaattacagTGCCGAACAACTGGTGGACATCGGCTGTCAATGGGTTATTCTTGGACACTCTGAGCGTAGACATATTATTGGTGAAAATGATGAG
upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 4
-----cggttttgaatgtgatgttcaagccaattatgttgttaccttcttgtggttctttgaacaagttcacttgtttacacttacttccacctgactctttaagTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
| |||| || |||| ||| |||| | ||| | | | | | | | | ||||| || | | | | | || |||| || ||||| ||| | || || | ||||||||||||||||| || ||||| |||||| | ||||| |||||||| |||
gggatggactttgtataatatgtaacagcggattaggagcttattatttcacttctagctttgctaatg-gcagttttacctttcccttaa----aatattacagTGCAGAACAACTGGTGGACATCGGTTGTCAATGGGTTATTCTTGGACACTCAGAGCGTAGACATATTATTGGTGAAAATGACGAG
upper sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G21170.2 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------cggttttgaatgtgatgttcaagccaattatgttgttaccttcttgtggttctttgaacaagttca-----cttgtttacactt-acttccacctgactcttta---agTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
|||| | | | | | | | | | ||| ||| || | | | | | | ||||| | | || | || | | | || ||||| || || ||||||||||||||||||||||| |||||||| ||||| || || |||||||| || |||||||| ||||||
gttacgacttctctttttcacttatactatatctctttttatttgattgaaattttttgacgaaaatattagagcgttgcaactaatccctccttatgactttccggtgtaatatatgaaccttgtctgaatttcaaagttgcccgttttaccatacagCGTGGAACAGCTCAAAGACCTTGGCTGCAAGTGGGTCATTCTTGGGCATTCCGAACGGAGACATGTCATCGGAGAAAAAGATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggttctttgaacaagttcacttgtttacacttacttccacctgactctttaagTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
ctcttt CT-rich tract
ttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cggttttgaatgtgatgttcaagccaattatgttgttaccttcttgtggttctttgaacaagttcacttgtttacacttacttccacctgactctttaagTGTGGAGCAACTAAAAGACCTTGGCTGCAAGTGGGTTATTCTTGGACATTCTGAGCGAAGACATGTAATTGGAGAAAATGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - -gaatgtg
- - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - -tgttacc
- - - - - - - - - - - - - - - - - - - - -tcttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttgt