Sequence
atgc intronic sequence ATGC exonic sequencegtaagggcacaaggcacatgttttcctgtaacttgatgaaaagcttgccatgtgattttgaatatatgttctccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccacattgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
Basic information
species | Glycine max |
transcript | GLYMA03G29280.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G047310_T02 (Zea mays), 3'ss of exon 6
gtaagggcacaaggcacatgttttcctgtaacttgatgaaaagcttgccatgtgattttgaata-tatgttctccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccacattgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
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-----------------------------------gtgagggatatacgat---atttggattggcaatttttccgtctgcctatttt--tttgtctctatttttat---ggtcttttttatgccagATGATGGGAAACTACAAGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACTGTGAGTGATGATGATGT
upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180988_T01 (Zea mays), 3'ss of exon 6
gtaagggcacaaggcacatgttttcctgtaacttgatgaaaagcttgccatgtgattttgaatatatgttctccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccacattgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
||| | || | ||| || | | || || |||| | | | | | | ||| | || |||||||||| || | | | ||||||||||| |||||||| ||||| || ||||| |||||||| || |||||||| || | | ||||| |||||| |
-----------------------------------gtgagggatatataatat----ttggattggcaatttggtcgtctggcttttttctctatctctattcttatggggttttt---atgccagATGATGGGAAATTACAGGCAGAGTCAGACTCTGGTGAATTCTGGGTCCTTTTTGGAGGTTTTGCACCAATTGGGAAAAAAACCGTGAGTGATGATGATGT
upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
-----gtaagggcacaaggcacat-gttttcctgtaacttgatgaaaagcttgccatgtgattttgaatatatgttctccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccac-attgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
|| |||| | | |||||| ||| | ||||| || || | | || | ||| ||| ||||| | | || | | | ||| | ||| | || ||||||| ||||| | ||||| || ||||| || |||| ||||||||| |||||||||||||||||||| || || | ||| | | ||| ||||| ||
gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacag--tgttttaatacttaaagaataggttt------tgtgtgtggaaacttatctatattcatac-----tttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACAT
upper sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gtaagggcacaaggcacatgttttcctgtaacttgatgaaaagcttgccat-gtgattttgaatatatgttctccaagtgtgtattt----tgatttgtttgtgactataaaaaggtatcccacattgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
| | || | ||| | | | | || || || | |||| || | |||| | | |||| || || || | | |||| | | | || |||||||||||||||||| | ||||||| |||||||||||||| ||||| || ||||||||||||||||||||||| || ||| | | || |||||| |
gtaagagcacatgcattaataacttgctgatgttagcttcgcttttagtacttatgtattcaatctctgaacagagctcatttgcattttcattcttaacatttgtaattgctactcttcattcattaacgtaaat-gatgtttgcaatgccagATGATGGAAAGCTGGTTGCTGAGTCTGACTCAGGTGAATTCTGGGTCCTGTTTGGTGGTTTTGCTCCCATTGGCAAAAAGGTTGCCACCGAAGATGATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccacattgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
ttttgat putative branch site (score: 4)
tattttgatttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggcacaaggcacatgttttcctgtaacttgatgaaaagcttgccatgtgattttgaatatatgttctccaagtgtgtattttgatttgtttgtgactataaaaaggtatcccacattgcagATGATGGAAAGCTGGATACTGAGTCAGACTCAGGTGAATTTTGGGTTCTCTTTGGTGGTTTTGCTCCCATTGGGAAGAAGATAATTAGTGAGGATGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG