Sequence
atgc intronic sequence ATGC exonic sequencegtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
Basic information
species | Glycine max |
transcript | GLYMA11G18400.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
gtttatatagtttcatctgctcaaatgat-tccaagctg-taaagtttgattatttgatta---ttttctttttggta-----tctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
||| |||| | | | | | || ||| || ||| |||||| | | || | | | || | | ||||||| ||||| ||| | |||||||| || || ||||| ||||||||||| || || ||||||||||| ||||||||| || | |||||
gttaatatttccttctgtttttttctcatatcctgtttgctaacacgcctttattttgtcaagcttatatgtatgtaaaatgttttgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 6
------------gttta-tatagtttcat-ctgctcaaatgattccaagctgtaa----agtttgattatttgattattttctttt--tggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
||| | || || || | || | || | || | | | |||| || || | || | | | | | | | | ||||| || || ||| | |||||||| || || ||||||||||||||||| ||||| ||||||||||| || |||||| || | |||||
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgatccagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 6
--------------gttta-tatagtttcat---ctgctcaaatgattccaagctgt-aaagtttgattatttgattattttctt-tttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
||| | || || || | | || | | | | || | |||| || || | || | | | | | | | | ||||| || || ||| | |||||||| || || ||||||||||||||||| ||||| ||||||||||| || |||||| || | |||||
cagatgatattgatgttgactagaggttggtgctttccttttggtacttgatccagtcatggtttcttttgttaaacatatgcgtatatagctttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G052515_T01 (Zea mays), 3'ss of exon 4
gtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttgg---tatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
||| | |||| | | | | ||||| | | |||| || || | || | | ||| | | | ||||| || || ||| | |||||||| || || ||||||||||||||||| ||||| |||||||| || || |||||| || | |||||
gttggtgc--tttccttttggtaccttgatccaatc---atggtttcttttgttaaacatatgcatttataactttttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAAAAGCTTAAGAACAACATCCGTTGGAA
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G029735_T01 (Zea mays), 3'ss of exon 3
------------gttta-tatagtttcat-ctgctcaaatgattccaagctgtaa----agtttgattatttgattattttcttttt--ggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA------------
||| | || || || | || | || | || | | | |||| || || | || | | | | | | | | ||||| | || ||| | |||||||| || || ||||||||||||||||| |||| | | || | | ||| || |||
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgattcagtcatggtttcttttgttaaacatatgcatatatagcttttttcagGTATAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACAT-CACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAG
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G22220.2 (Arabidopsis thaliana), 3'ss of exon 4
-----gtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
| | | | | | || | | |||| || | ||| || ||| ||| | ||| | |||||| |||||||| ||||||||||||||||| ||||| | ||||| || || | ||||| |||| || |||||| | ||||| |||||
gtgacatatttgaactctagactcccatattgatgtattactttctgtcaaacttagctg--tatgttcctgttgat----gcagGTACAAAAGAGAAGGATATATGATATAACCAATGTGTTAGAAGGAATAGGTTTGATAGAGAAGACGCTTAAGAACAGGATTCAGTGGAA
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g01110.t01 (Vitis vinifera), 3'ss of exon 4
gtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
| ||| | | | ||| || | | ||| | | | |||| |||| || ||| ||||| || |||||| | |||||||| ||||||||||| |||||||| ||||| || || || ||||| | ||||| ||||||| |||||
-gtgctattttatatctaacgcaatatatcctgtggcataacatcctgtcaattgaaacgtttccatt----atc-acagGTACAGAAGAGGCGTATATATGACATAACAAATGTCCTTGAAGGAATTGGTCTCATTGAGAAGAAGTTGAAGAATAGAATTCAGTGGAA
upper sequence: GLYMA11G18400.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S38_356V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtttatatagtttcatctgctc-----aaatgattccaagctgtaaagtttgatt-----atttgattattttc--tttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
| | ||| |||||| | | |||| | | | | | ||| | | || || || | | | || ||| || ||||| ||||||||||||||||||||||| || ||||| | || || ||||| | || || ||||| || ||||| ||||| ||||||
tatgtagcgctgttatcctttcatttatttcaagtaaataactacctctttttaagctgttctctgacatcagacgatgtacaatcttgggtttcaccagGTACAAAAGAGGAGGATATATGATATTACCAATGTATTGGAGGGAATTGGGTTAATTGAGAAGAAGCTAAAGAATCGAATCAGATGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
atttgat putative branch site (score: 5)
taaagtttgattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttatatagtttcatctgctcaaatgattccaagctgtaaagtttgattatttgattattttctttttggtatctgcagGTGCAAAAGAGGAGGATATATGATATAACAAATGTTCTTGAAGGGATTGGACTTATAGAAAAGAAACTCAAGAACCGAATTCAATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC