Sequence
atgc intronic sequence ATGC exonic sequence...atttccatgataactagatatcgtttctcaattgatgtcatctttgcatagttttgcatttggagttttaattttgaccttaactgtcaattctgattagGACATTTGACATCAAAAAGTGATGTCTATAGTTTTGGAGTAGTGCTACTTGAAATGCTCACTGGCCGACGATCTATCGATAAAAATAGACCAAACGGGGA
Basic information
species | Glycine max |
transcript | GLYMA09G37580.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 5
atttccatgataactagatatcgtttctcaattgatgtcatctttgcatagttttgcatttggagttttaattttgaccttaactgtcaattctgatt---agGACATTTGACATCAAAAAGTGATGTCTATAGTTTTGGAGTAGTGCTACTTGAAATGCTCACTGGCCGACGATCTATCGATAAAAATAGACCAAACGGGGA
| |||| | | | | || || || ||| |||| |||| || | || | | | | | ||| || ||| |||||||||||||| |||||||||||||||||||| || ||||||||||| ||| | | || || | || || || || || | ||||| || ||
-tgcaaatgaagttcaaacacagatttgttgcctttggtat-tttatgcgatttt-cattatgactcttggtataattttcttgtattttttccacttttcagGCCATTTGACATCAAAGAGTGATGTCTATAGTTTTGGTGTGGTGCTACTTGAGATGATGTCAGGGCGCAGGTCAATGGACAAGAACCGCCCAAATGGTGA
upper sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 5
atttccatgataactagatatcgtttc-tcaattgatgtcatctttgcatagttttgcatttggagttttaattttgaccttaactgtcaattctgattagGACATTTGACATCAAAAAGTGATGTCTATAGTTTTGGAGTAGTGCTACTTGAAATGCTCACTGGCCGACGATCTATCGATAAAAATAGACCAAACGGGGA
| | | | ||||| || ||| ||| ||| | || ||| | ||| | | ||| |||| | || | ||| || ||||||||||| || ||||| ||||||||||| || || |||||||||||| | ||||| ||||||||||| || ||||| | ||||| || ||
--------gtgagtcctctttggtttcatccattttcttcaacttgaaaacattcaatgtttacatctttgttgatttgcttc-ctgttgaacttgttaagGTCACTTGACATCAAAGAGCGATGTTTATAGTTTTGGGGTGGTTCTACTTGAAATGTTGACTGGACGACGATCTATGGACAAAAACCGCCCAAATGGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatagttttgcatttggagttttaattttgaccttaactgtcaattctgattagGACATTTGACATCAAAAAGTGATGTCTATAGTTTTGGAGTAGTGCTACTTGAAATGCTCACTGGCCGACGATCTATCGATAAAAATAGACCAAACGGGGA
ccttaac putative branch site (score: 3)
agttttaattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttccatgataactagatatcgtttctcaattgatgtcatctttgcatagttttgcatttggagttttaattttgaccttaactgtcaattctgattagGACATTTGACATCAAAAAGTGATGTCTATAGTTTTGGAGTAGTGCTACTTGAAATGCTCACTGGCCGACGATCTATCGATAAAAATAGACCAAACGGGGA
- - ccatgat
- - - - - - - - - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaac