Sequence
atgc intronic sequence ATGC exonic sequence...ttctgcagttatatttctcaaagctgagatggtttacttgttagaaaacactctttgacatattttaaccagcgtcgctcaaatgaatttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
Basic information
species | Glycine max |
transcript | GLYMA02G04360.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g37990.1 (Oryza sativa), 3'ss of exon 3
ttctgcagttatatttctcaaagctgagatggtttacttgttagaaaacactctttgacatattttaaccagcgtcgctcaaatgaatttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
|| | || | || || | | || || || |||| | | || | ||| | | || | || || ||||||||||||||||||| ||||| || ||||| || | |||||| |||||||| ||||||||||||| ||| | || |||| | ||||| || |
-------gtaaggatttgtgtgagaaacattgtatcgtcgtgcaaactcaaacttt----ctgtgtgactgacactgct-ggacgcatgt--ttgttcagGTTAGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGGTACAAGCTCGTACCTGGTTCAAGCTGTCTTCCACTGGCCCTGCCTGAGGCGAAAT
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 9
ttctgcagttatatttctcaaagctga-gatggtttacttgttagaaaacactctttgacatattttaaccagcgtcgctcaaatgaatttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
| | | || | | || || | || | | || || | ||| | || | | | | || | |||| ||||||||||||| ||||| || ||||| || | |||||| |||||||| ||||||||||||| ||| | || ||||| | ||||| || |
-catatgatcaaatattgcgaaaatgtcaacggcatcgtacataatgaaactgaggtagtatacatgcacgttgatacactgttttatgcacgttgatcagGTACGGAACACAAGGACTGTAAATCGTACTGGACAACCAACAGGCTACAAGCTCATACCTGGTTCAAACTGTCTTCCGTTGGCCCTGCCTGAGGCGAAAT
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 9
ttctgcagttatatttctcaaagctgagatggtttacttgttagaaa-acactctttgacat-attttaaccagcgtcgctcaaatga-atttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
|| || | | | ||| || ||||| || || ||| | | ||| | ||||| | |||| ||| | || || | || |||||||| || || ||| | ||||||||||||||||| |||||||| ||||||||||||||||||||||| || |||||||| ||||| || |
tttcctgattgggtgttt--aaggtg-gatggaatatccattctttgtacatttgaagtcattaaattaacttcttgttcatgtatgatgttttatcattcagATCAGAAACACAAGAACTGTCAACAGGACTGGGCAGCTAACAGGTTACAAGCTGGTACCTGGTTCAAATTGTTTACCATTAGCTGGTTCTGAGGCAAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacactctttgacatattttaaccagcgtcgctcaaatgaatttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
ttttaac putative branch site (score: 2)
tttcttttttt putative PPT
tcaaatgaatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgcagttatatttctcaaagctgagatggtttacttgttagaaaacactctttgacatattttaaccagcgtcgctcaaatgaatttctttttttagGTTAGGAACACAAGGACGGTAAACCGAACTGGGCAGCTAACAGGATACAAGCTAGTACCTGGTTCAAATTGTTTACCCTTGGCTGGTTCAGAGGCCAAGT
ttctgca
- - - - - - - - - - - - - -gatggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaccagc