Sequence
atgc intronic sequence ATGC exonic sequence...aattcgatcttgtatgtatttttgtctagctagtcttaatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgtgaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
Basic information
species | Glycine max |
transcript | GLYMA11G03420.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G03420.2 (Glycine max), 3'ss of exon 7
lower sequence: AT4G22540.3 (Arabidopsis thaliana), 3'ss of exon 5
aattcgatcttgtatgtatttttgtctag--ctagtct-taatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgtgaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
|| | | ||||| | ||| | | || |||| | | | | | | || || | || |||||||||||||||| ||| | || ||||||||||| ||||||| ||| ||||||||||||| |||||| ||| || |||||||||||||| ||||| |
----gtatgtcacacaaattttaactcaaatttagaatgtgatgaacataattgttagaatctttaccaagactagagaatatcattcttttggttataatagGTCAGTCACCATCCAACTGTTATCGCCTGCCACTGTGAAGGTAAAGGGTGGAAGTTTTGGGGTGACACTAACCTCAGGTCAAAGTTTTGGGGGAGGTCGA
upper sequence: GLYMA11G03420.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
-aattcgatcttgtatgtattt--ttgtctagctagtcttaatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgt-gaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
||| ||| || || | || |||| || ||| | | | |||| | | || | | | || | || | | | ||||||||| ||||| || || || |||||||||||||| || ||||||| ||| ||||| || |||||||||| ||| | | |||| ||||||||| | ||||
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcac----cccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA
upper sequence: GLYMA11G03420.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
-aattcgatcttgtatgtattt--ttgtctagctagtcttaatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgt-gaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
||| ||| || || | || |||| || ||| | | | ||| | | || | | | || | || | | | ||||||||| ||||| || || || |||||||||||||| || ||||||| ||| ||||| || |||||||||| ||| | | |||| ||||||||| | ||||
ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcac----cccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caattcatcaacctgccaatatatttcacgttccctgacattatgtgtgaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
ccctgac putative branch site (score: 3)
aatatatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattcgatcttgtatgtatttttgtctagctagtcttaatatgtgcaattcatcaacctgccaatatatttcacgttccctgacattatgtgtgaaacagGTCAGTCACCATCCGACTCTCATTGCCTGCCACTGCGAAGGTAGAGGATGGAAGTTTTGGGCTGACACCAACATCCATTCAAAGTTTTGGGGAAGGTCAA
- - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgcc