Sequence
atgc intronic sequence ATGC exonic sequencegtgatattttatctgaatttatttttgtgttgcagaaatgttcataaattcatatactaattatagcttttcttctgcagGAGCTTTTGATGGTGTGCTTGAGTTTTTGATTCAGTCTGGAAAAAGTCTCCCTGAAGCTGTTATGTTGATGATTCCTGAAGCATGGCAAAATGACAACAA
Basic information
species | Glycine max |
transcript | GLYMA04G41540.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G41540.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0055g00620.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------------------gtgatattttatc----tgaatttatttttgtgttgcagaaatgttca--taaattcatatactaattatagct-------------------tttcttctgcagGAGCTTTTGATGGTGTGCTTGAGTTTTTGATTCAGTCTGGAAAAAGTCTCCCTGAAGCTGTTATGTTGATGATTCCTGAAGCATGGCAAAATGACAACAA
| ||| | || ||||| || | | | ||| | || | ||| || | || || || ||| | | ||||||||||||||| || |||||| || || ||| | || | ||||||||| |||||||| ||| ||||||| ||||||||||||||||||||||| ||
gttagattgtaattcaacattttgtatatatatgcacagtcattgatatatatcaatacaagtatgaacccatgtgttttactatctaattcctatgaatacatgaatcattggtggaagcatgcaggtgcattttcatgccttttttaactggcttgtgtttgaattttgtttgctttatagGAGCTTTTGATGGCGTTCTTGAGCTTCTGGTTCGAGCAGGCAGAAGTCTCCCCGAAGCTGTCATGATGATGATACCTGAAGCATGGCAAAATGACAAGAA
upper sequence: GLYMA04G41540.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g00530.t01 (Vitis vinifera), 3'ss of exon 1
------------------------------------------------------------------------------gtgatattttatc----tgaatttatttttgtgttgcagaaatgttca--taaattcatatactaattatagct-------------------tttcttctgcagGAGCTTTTGATGGTGTGCTTGAGTTTTTGATTCAGTCTGGAAAAAGTCTCCCTGAAGCTGTTATGTTGATGATTCCTGAAGCATGGCAAAATGACAACAA
| ||| | || ||||| || | | | ||| | || | ||| || | || || || ||| | | ||||||||||||||| || |||||| || || ||| | || ||||||||||| |||||||| ||| ||||||| ||||||||||||||||||||||| ||
gttagattgtaattcaacattttgtatatatatgcacagtcattgatatatatcaatacaagtatgaatccatgtgttttactatctaattcctatgaatacatgaatcattggtggaagcatgcaggtgcattttcatgccttttttaactggcttgtgtttgaattttgtttgctttatagGAGCTTTTGATGGCGTTCTTGAGCTTCTGGTTCGAGCAGGTAAAAGTCTCCCCGAAGCTGTCATGATGATGATACCTGAAGCATGGCAAAATGACAAGAA
upper sequence: GLYMA04G41540.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------------------------------------gtgatattttatc----tgaatttatttttgtgttgcagaaatgttca--taaattcatatactaattatagct-------------------tttcttctgcagGAGCTTTTGATGGTGTGCTTGAGTTTTTGATTCAGTCTGGAAAAAGTCTCCCTGAAGCTGTTATGTTGATGATTCCTGAAGCATGGCAAAATGACAACAA
| ||| | || ||||| || | | | ||| | || | ||| || | || || || ||| | | ||||||||||||||| || |||||| || || ||| | || | ||||||||| |||||||| ||| ||||||| ||||||||||||||||||||||| ||
gttagattgtaattcaacattttgtatatatatgcacagtcattgatatatatcaatacaagtatgaatccatgtgttttactatctaattcctatgaatacatgaatcattggtggaagcatgcaggtgcattttcatgccttttttaactggcttgtgtctgaattttgtttgctttatagGAGCTTTTGATGGCGTTCTTGAGCTTCTGGTTCGAGCAGGTAGAAGTCTCCCCGAAGCTGTCATGATGATGATACCTGAAGCATGGCAAAATGACAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgttgcagaaatgttcataaattcatatactaattatagcttttcttctgcagGAGCTTTTGATGGTGTGCTTGAGTTTTTGATTCAGTCTGGAAAAAGTCTCCCTGAAGCTGTTATGTTGATGATTCCTGAAGCATGGCAAAATGACAACAA
tactaat putative branch site (score: 1)
cttttcttctgc putative PPT
aaatgttcataaattc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatattttatctgaatttatttttgtgttgcagaaatgttcataaattcatatactaattatagcttttcttctgcagGAGCTTTTGATGGTGTGCTTGAGTTTTTGATTCAGTCTGGAAAAAGTCTCCCTGAAGCTGTTATGTTGATGATTCCTGAAGCATGGCAAAATGACAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC