Sequence
atgc intronic sequence ATGC exonic sequence...ctaaattgatatagtaaaaagtagcatcggtatcctttgaattatgcaagtttaatggctgctctaagtattcggttttggttttaactttaacttacagAATGAGTGTCGAGCAATTGGGGTTCAACAGAGCCGTGGTTGGGTTCATTATGCAATTCATCGACCTGAGCCACAAATAATGCTTTTCAGGAGGCCTTTGA
Basic information
species | Glycine max |
transcript | GLYMA12G08890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27970.1 (Arabidopsis thaliana), 3'ss of exon 3
ctaaattgatatagtaaaaagtagcatcggtatcctttgaattatgcaagtttaatggctgctctaagtattcggttttg--gtttta--actttaacttacagAATGAGTGTCGAGCAATTGGGGTTCAACAGAGCCGTGGTTGGGTTCATTATGCAATTCATCGACCTGAGCCACAAATAATGCTTTTCAGGAGGCCTTTGA
| | ||||| | | | || | | | | ||||| || | | |||| | ||||| |||||| | | || ||| ||| || |||| || || || || || || ||||| ||||||||||| || |||||||| ||||||||||| || ||||| || ||||||||| | |
--tgacgaagatagtttagatatttttttgtgttatcagtcaattctcagttttctgatt--ttgaagttaacagttttcttgttttacaatctggttttgtagAGTGAATGGAGAGCCATCGGAGTGCAGCAAAGTCGTGGATGGGTTCATTACGCGATTCATCGTCCTGAGCCACATATCATGCTCTTTAGGAGGCCTCTTA
upper sequence: GLYMA12G08890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27960.1 (Arabidopsis thaliana), 3'ss of exon 2
ctaaattgatatagtaaaaagtagcatcggtatcctttgaattatgcaagtttaatggctgctctaagtatt--cggttttggttttaacttt----aacttacagAATGAGTGTCGAGCAATTGGGGTTCAACAGAGCCGTGGTTGGGTTCATTATGCAATTCATCGACCTGAGCCACAAATAATGCTTTTCAGGAGGCCTTTGA
||| | | |||| | || || || | |||| || ||||| | | | || | || ||| ||| |||| || || | | |||| || || ||||| || || || || || ||||| || ||||| ||||| || |||||||||||||||| || |||||||| |||||||||||| | |
-taa---ggtttagtgataaagag-attttagacatttgtgttgtgcaa-tctcttcaatgttgtattgattggtggtgatggtaaaaatgtttggaatttcgaagAACGAATGGCGAGCGATAGGAGTGCAGCAAAGCCGCGGATGGGTACATTACGCGGTTCATCGACCTGAGCCGCACATAATGCTATTCAGGAGGCCTCTTA
upper sequence: GLYMA12G08890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 3
ctaaattgatatagtaaaaagtagcatcggtatcctttgaattatgcaagtttaatggctgctctaagtattcggttttggttttaact--ttaacttacagAATGAGTGTCGAGCAATTGGGGTTCAACAGAGCCGTGGTTGGGTTCATTATGCAATTCATCGACCTGAGCCACAAATAATGCTTTTCAGGAGGCCTTTGA
|| | | |||| ||| | | || || || || || || | | ||| |||| || | || |||||||| || || || ||||||||||| ||||||||||| ||||| || |||||||||||||| ||||||||||| || ||||| |||||||||||| |||
ctctttctgcttc-taaacagtgcggttttttctattgaaaaagaaaaaaatttcaatcttctgcagccctaaagttgatattttgttgggttgattt-cagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTATGCAATTCATCGCCCTGAGCCACACATCATGCTCTTCAGGAGGCCTCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaagtttaatggctgctctaagtattcggttttggttttaactttaacttacagAATGAGTGTCGAGCAATTGGGGTTCAACAGAGCCGTGGTTGGGTTCATTATGCAATTCATCGACCTGAGCCACAAATAATGCTTTTCAGGAGGCCTTTGA
ttttaactttaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaaattgatatagtaaaaagtagcatcggtatcctttgaattatgcaagtttaatggctgctctaagtattcggttttggttttaactttaacttacagAATGAGTGTCGAGCAATTGGGGTTCAACAGAGCCGTGGTTGGGTTCATTATGCAATTCATCGACCTGAGCCACAAATAATGCTTTTCAGGAGGCCTTTGA
- - - - - - - -aaaaagta
- - - - - - - - - - - - - - - - tcctttg
- - - - - - - - - - - - - - - - - - - - - - tgcaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg