Sequence
atgc intronic sequence ATGC exonic sequencegtagggctaatttctgttccgtagagggcttcaatttgcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggacttaattccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
Basic information
species | Glycine max |
transcript | GLYMA09G40480.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8
gtagggctaatttctgttccgtagagggcttcaattt--gcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggacttaattccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
||| || ||| | | | | | |||| |||| | | |||| | || || | | | || | || | || | ||| ||| | || ||||| || ||||||| ||||||||||||| ||||| |||||||||||||| ||||||||||| ||||||||| | || || |||||||| | ||| ||||
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctc----tgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
gtagggctaatttctgttccgtagagggcttcaatttgcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggactta---attccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
||| | | | ||| | ||| | || | || ||| | | ||| | || | | | | | || ||| | ||| | ||| || ||||| || | |||||| |||||||||| |||||||| |||||||| |||| ||||||||||| || |||||| | || || |||||||||| ||| ||||
gtatgac-accttcactcatgta-----ccataactcttatctaaa--------gacctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 8
gtagggctaatttctgttccgtagagggcttcaatttgcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggactta-attccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
| ||| | ||| | || | | | | | | ||| | || | |||||| ||| ||| || ||||| || || |||||||||||||| ||||||||||| ||||| | || | ||||||||||| ||||||||||||||||| || || |||| ||||||||
-----------------------gtaggcatttatt-----gtaattttctggtaaccacattaatttaagaattttttggtttactcacaatgtgttttcttccgttgcagGTTTTTACCACAGCGGCATATGACGACCACAAAAATATTGTGTTTTTGTCCTTTGAAATTATCGAGAAGATTATTCGAGAATATTTCCCATACATCACTG
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------gtagggctaatttctgttccgtagagggcttcaatttgcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgct--tgtggac-ttaattccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
| | | | | | | || | || || | | | | | || | | ||| | || ||| | |||| | || || ||||| ||||||||||| || |||||||| || |||||||| ||||||||||| |||||||| || ||||||||| | ||||| ||||| || | ||| ||||
gtattgaaatctgtccaatctgtagttttctattaaagaatatgcaagtgagggagtgattttagttcttcaatttgatttcatcattgattttatttggtgaatggctatgttaacagattattaatgtgaatatttttttcagGTCTTCACAACAGCAGCTTATGATGATCATAAAAACATAGTACTCCTGGCCTTTGAAATAATTGAGAAGATTGTGCGAGACTACTTCCCCTACATTACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgctgaagtttttctttcattatttctactcattgcttgtggacttaattccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
acttaat putative branch site (score: 4)
tttttctttcattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagggctaatttctgttccgtagagggcttcaatttgcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggacttaattccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA