Sequence
atgc intronic sequence ATGC exonic sequencegtaagagggctagctacaacttctgctctatctttctttttttttttttttgtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaattagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
Basic information
species | Glycine max |
transcript | GLYMA02G10620.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G10620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G28990.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagagggctagctacaacttctgctctatctttctt-----tttttttttttttgtttgatcatatataccccttt-catgatcgttgtgacatgct-tggataaaat-tagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
|||| | | | | | | | | ||| ||| |||| || || || | | | | ||| | || || | | | |||||||| |||||||| |||| ||||||| |||| ||||| || || |||||||||||||||||||| || ||||||| || || || |||| || |
gtaataactcgaacatgtgcatgcgtttcttctcatgaaggaacagtttcttttaggtacattcttaagggtatatatataaaaacgtgatagtgtgtcatgtgttatgtatagGTGCAACACATGATAGAGACATGTTTGACCTTTAACATGAGCAAAGAGGAATGCATGGAAGCTCTCTCAGAGAATGCAAACATCAATCCCATCATCACGT
upper sequence: GLYMA02G10620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
----------------gtaagagggctagctacaacttctgc--tctatctttctttttttttttttttgtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaattagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
|||| | ||| || | || || || | | | || | | || | || || ||| ||| ||| || || | || ||||||||||||||||| ||||| ||||||||||| || ||| || ||||| || ||||||||||||| ||||||||||| || | |||||||| || |
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttg-gatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
upper sequence: GLYMA02G10620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0036g00440.t01 (Vitis vinifera), 3'ss of exon 1
gtaagagggcta----gctacaacttctgctctatctttctttttttttttttttgtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaattagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
||| | || ||| || || | || | |||| ||||| | | | ||| | | | | | | || || || ||||||||| ||| |||| ||||| ||||||||||| |||||| | || ||| | ||||||||||| || ||||| ||||| | || | || ||||| || |
gtagctgaattataacattactcctcacatgggattctactgtgattttgtttttagcaaaccttctatctctttattgttttgttgatgttgtggcctgact--tttagGTGCAACACCTGATCGAGAAATGTTTGATCTTCCACATGACCAAAGAACAGTGCATGGAAGCCCTTTCCAAACATGCTGACATCCAACCAGTCATCACGT
upper sequence: GLYMA02G10620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0317g00030.t01 (Vitis vinifera), 3'ss of exon 1
gtaagagggctagctacaacttctgctctatctttcttttttttttttttt--gtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaat-tagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
||| ||| | | | ||||| | | | ||||| | | | | | | | || || | || | || | |||| || ||| | || ||||| ||||||||||| |||||| || ||||| ||||||||||| |||||||| |||||||| || | || ||||| || |
---------------gtgactcaaatcatatgtaacatcatttttcatgcccaggtctcccatatttgatcttgtttttgctgatatgtattggtgggttgaattgcagGTACAACACCTAATAGAGAATTGTTTGATCTTCCACATGAGTAAAGAAGAGTGCATGGAAGCCCTCTCCAAACATGCAAACATCGAACCCGTCATCACCT
upper sequence: GLYMA02G10620.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0317g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtaagagggctagctacaacttctgctctatctttctttttttttttttttgtttgatcatatatacccctttcatgatcgttgtga-catgcttggataaaat-tagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
|| | | |||| ||| ||||| ||| |||| || || | | | | || | || ||| | || ||| | | | |||||||| ||| |||| |||||||| |||||||| |||||| || ||||| ||||||||||| |||||||| |||||| | || || | ||||| || |
-----------gttcctaattattctcctatatttgatttttgtttctttttttctttctttttcgtttactac-tgttttttatgatcttgggtggttgatttgtagGTGCAACACCTGATAGAGAAGTGCTTGATCTTCCACATGAGTAAAGAAGAGTGCATGGAAGCCCTCTCCAAACATGCAGACATCAACCAAGTCATCACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaattagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
gtttgat putative branch site (score: 5)
ataaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagggctagctacaacttctgctctatctttctttttttttttttttgtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaattagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG