Sequence
atgc intronic sequence ATGC exonic sequencegtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatgatccgctctgcctttgtgcaacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
Basic information
species | Glycine max |
transcript | GLYMA15G04230.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04230.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g05430.1 (Oryza sativa), 3'ss of exon 1
gtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatg-atccgctctgcctttgtgcaacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
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-----------------------------------gtttgatctcagatctatgcatttattttacacaaatcctactg-cattt-cttgttgctaattgcattcttgtttaataatccagTTTGCAGCATTATTAACTCTAGTCATAATCATTCTCATCAACTTGGCTGTTGGGATTCTTCCACATGTTGACAACTTTGCTCATCTTGGAGGATTTACAT
upper sequence: GLYMA15G04230.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G100889_T01 (Zea mays), 3'ss of exon 3
gtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatgatccgctctgcctttgtgcaacagacatttatttcttttcc--attttatgtttgtattgtttt--gcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
| | |||| || || | || |||| | | | |||| | ||| ||| |||| | | ||||||||||| | ||||||| | | ||| || | ||||| ||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| | |
----------------------------------------gtcgattctaaaatatatgcagtattttcacaaaacattccatattccatttttctaattctattcttgtttcgaaaaaaacagTTTGCAGCACTCTTGACTCTAGTTATGATCATTCTCATCAACTTAGCTGTTGGGATCCTTCCACATGTTGACAACTTCGCTCACCTTGGAGGATTTATGT
upper sequence: GLYMA15G04230.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G29050.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatgatccgctctgcctttgtgcaacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
| | ||| | | || |||| | |||| || | || | | | || | | | |||| | | ||||||||||||||| | |||| || || ||||| | | || |||||||| || || |||||||||||||| ||||| ||||| ||| |||||||||| |
--------------------------gtagccaaatcttcccttgt--taaacaagccgcactttcgatgaatga--------tgtgtcaataatgtcattggtttttctacatttgcagTTTGCAGCTCTTTTGACACTCATCTTCATCATAGCCATTAATTTAGCAGTAGGTATTCTTCCACATGTAGACAACTTTGCCCATCTTGGAGGATTCACAT
upper sequence: GLYMA15G04230.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04890.t01 (Vitis vinifera), 3'ss of exon 3
gtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatgatccgctctgcctttgtg--caacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
| || || || ||||| | | | | || ||| || | | || | | || | | | ||| ||| || | || | || | ||||||||||| ||| ||||||| || ||||| | || ||||| |||| || || || || |||||||||||||| ||||||||||||||||||||||| |
-----gtacttaataactgctctcaatg-acttgaggttccttttgaaaatttcatttctttggagttagctacttatgggggcctatatctcacagtttcagttatttttttaatgctcagTTTGCAGCATTATTGACTCTCATTCTCATCATCATAGTCAATCTAGCAGTGGGGATCCTCCCACATGTGGACAACTTTGCTCATATTGGAGGATTTGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgtgcaacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
ttgtttt CT-rich tract
atttatttcttttcca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatggatcaaaaaatgtgttcaattcaatagtgcttgcttcgtaataaatgatccgctctgcctttgtgcaacagacatttatttcttttccattttatgtttgtattgttttgcagTTTGCAGCGTTACTGACTCTTATAGTCATCGTTGTAATCAATTTAGCTGTTGGAATTCTTCCACATGTGGACAATTTTGCTCATATTGGAGGATTTGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT