Sequence
atgc intronic sequence ATGC exonic sequence...acataggtgtatatatgtaagacatctatgaaaactatattatgacgctaatttctctgcaagcctttctttttatgaggccattctaaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC
Basic information
species | Glycine max |
transcript | GLYMA20G24040.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
acataggtgtatatatgtaagacatctatgaaa-actatattatgacgctaatttctctgcaagcctttctttttatgaggccattctaaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC
|| || | | | | |||| | | || | | | | || | | || | | || || | || ||||| || | || || |||||||| ||||| || |||||||||||||| ||| || |||||||||||| || || ||||| | ||| || ||||
-tattgggttgttggccaagtgtttatatgttccgatgctgtgtgctgtttctgaccttgaatgatttggataaacatacacctttttctgtattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 12
lower sequence: AT2G16950.1 (Arabidopsis thaliana), 3'ss of exon 12
acataggtgtatatatgtaagacatctatgaaaactatattatgacgctaatttctctgcaagcctttctttttatgaggccattctaaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC
|| |||| | ||||| || | | |||| |||| || | | | || || | || |||||| || ||||| ||| ||| ||||| || |||||| | |||||||||||||| |||||||| || ||||| | ||||| ||||| ||||||||||| |
----------gtaaatgttattcatct-tggtctttttgaaatgaacacaatta----gctaaaccctgttcttctaag---------------ctgcagAAAAATTTATCAGCTTCTGGTGATGAGGCCTGGAAACAAAGGGAAGCTGCTGTTTTGGCTCTCGGCGCTATTGCTGAAGGCTGCATGAATGGTCTTTACC
upper sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 12
acataggtgtatatatgtaagacatctatgaaaactatattatgacgctaatttctctgcaagcctttcttt----ttatgaggccattct----aaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC
| |||| || | ||| || | || || | || | | | |||| ||||| | ||| || ||| | ||| |||||||||||||||||||||||| || || ||||| | |||||||| ||||||||||| || || |||||||||||| ||| || |||||||| | |||||||||||
aaatagaagt-----taaaagttatatgtgt---ctcaaccattagtttcacttctttgcaaccatttacttgtgtttaaaatatgatttccttaaaaatttctgcagGCTAAGTTATCAACTACTGATGATGAGACCTGGAAAGAAAGGGAAGCTGCCGTTTTAGCTCTTGGTGCTGTAGCTGAGGGTTGCATTACTGGTCTTTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctaatttctctgcaagcctttctttttatgaggccattctaaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC
ttctaaa putative branch site (score: 2)
tttctgc CT-rich tract
attctaaaatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acataggtgtatatatgtaagacatctatgaaaactatattatgacgctaatttctctgcaagcctttctttttatgaggccattctaaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC
- - - - - - - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccattct