Sequence
atgc intronic sequence ATGC exonic sequencegtaggtttatgtgtgcaatatatattttattgatgcaaaatatattggaatttttgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC
Basic information
species | Glycine max |
transcript | GLYMA04G38660.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaggtttatgtgtgcaatatatattttattgatgcaaaatatattggaattt--ttgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC
|||| || | || | || | | || | | | | | | | || | | ||| ||| | | || || || | | |||| | | || |||||| | |||||| || |||| || ||||||||||| |||||| | |||||| ||||||| ||||||||||| |||||||| ||
gtagtgcaatttctgaggttcatgatgtgaccata-atattctgtcgctacgcactttattttcatgtctttttaccttggtcacatactgaaacctcctgaattgtaaagCTCCAGCTTCCCAATCTGGTGGGTTTCAAGATGTTGATGGAGAAACTGAAGAGAGACGACGTGCCAGGCTGGAACGTCACCAGAGGACACAGGAGCGGGC
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 3
---gta-ggtttatgtgtgcaatatatattttattgatgcaaaatatattggaatttttgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC
|| ||| || | || ||| | | || || | || |||||| |||| |||| |||| | || | || || | | |||| | | || |||||| | |||||| || |||| || ||||||||||| |||||| | ||||| ||||||||||||||||||| |||||||| ||
gtagtgcaatttctgaggttcatccataatattctgtcgctgtgcacttt---atttttatgtcttttaactt------gctcaccta--ctgaaaccccctgtgttgtaaagCTTCAGCTTCCCAATCTGGTGGGTTTCAAGATGTTGATGGAGAAACTGAAGAGAGACGACGTGCCAGACTGGAACGCCACCAGAGGACACAGGAGCGGGC
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G12770.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaggtttatgtgtgcaatatatattttattgatgcaaaatatattggaattt--ttgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC-
|||| || | || | || | | || | | | | | | | || | | ||| ||| | | || || || | | |||| | | || |||||| | |||||| || |||| || ||||||||||| |||||| | |||||| ||||||| ||||||||||| |||||||| ||
gtagtgcaatttctgaggttcatgatgtgaccata-atattctgtcgctacgcactttattttcatgtctttttaccttggtcacatactgaaacctcctgaattgtaaagctccagCTTCCCAATCTGGTGGGTTTCAAGATGTTGATGGAGAAACTGAAGAGAGACGACGTGCCAGGCTGGAACGTCACCAGAGGACACAGGAGCGGGCT
upper sequence: GLYMA04G38660.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0188g00210.t01 (Vitis vinifera), 3'ss of exon 2
gtaggtttatgtgtgcaatatatattttattgatgcaaaatatattggaatttttgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC-
|||| ||| | | | | | ||||| ||| || || || || | |||| ||| ||| | ||| || | ||| ||| || | || | | ||| | ||| | ||||||||||| | || || || |||||||| ||| |||||| |||| ||||||||||||||||| ||||| ||||||||||||| |||
gtagctttctttccaaagtgaa-attttcttg-tgtaacatttaat--catttgtgatcctct-ctcttgtaagacttctaattggcttaactatttttta--ttgcaaaagCTGCTCCATCATCTGGAAAATTCCAAGAAGTTGAAGGGCAAAGTGAAGACCGACGGAGAGCCAGGTTGGAACGTCACCAAAGGACTCAGGAGCATGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC
cacttac putative branch site (score: 2)
ctctttttgtctcttt putative PPT
ttacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtttatgtgtgcaatatatattttattgatgcaaaatatattggaatttttgagtctcaacacttacaaaagctctttttgtctcttttcttctatgatttgaagCCGCTCCATCATCATCTGGAGAGTTTCAGGAGATTGAAGGGGAAACTGAAGAAAGACGAAGAGCCAGGTTGGAACGCCACCAGAGGACTCAGGAGCGTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA