Sequence
atgc intronic sequence ATGC exonic sequence...cattttatgggcatacttgatatgttttctaatcaattgattttaatattttacgtagcattgtttgttaagtattactgttaacctccatgttctccagGTTGCCAAAGAGAACGCGGATGTGATTGTAATGGATGATAACTTCACAACCATAGTGAATGTTACCAGATGGGGCCGTGCTGTTTATATTAATATACAAA
Basic information
species | Glycine max |
transcript | GLYMA09G35970.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g41580.1 (Oryza sativa), 3'ss of exon 4
catt--ttatgggcatacttgatatgttttctaatcaattgattttaatattttacgtagcattgtttgttaagtattactgttaacctccatgttctccagGTTGCCAAAGAGAACGCGGATGTGATTGTAATGGATGATAACTTCACAACCATAGTGAATGTTACCAGATGGGGCCGTGCTGTTTATATTAATATACAAA
| || | | || | || ||| || |||||||| | || | || | | |||| | || | | | | |||||||| ||||||| ||| ||||| || |||||||||| || ||| |||||| || |||||| | |||||||||||||| ||||| | || || || |
ccttggctgtaacagtattcatcattgtttagtgacatttgatttt--ccgtgtatgatatatctgtggacaagttgtgatgcaagttttatctgtttgcagGTTGCAAAAGAGAGCGCTGATGTTATAATAATGGATGACAATTTCGAAACCATTGTAAATGTTGCTAGATGGGGCCGTGCAGTTTACTTAAACATCCAGA
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------cattttatgggcatac-ttgatatgttttct-----aatcaa-ttgattttaatattttacgtagcattgtttgttaagtattactgttaacctccatgttctccagGTTGCCAAAGAGAACGCGGATGTGATTGTAATGGATGATAACTTCACAACCATAGTGAATGTTACCAGATGGGGCCGTGCTGTTTATATTAATATACAAA
|||| | ||| | ||| ||| ||| || ||||| | ||| | | | ||| | || | | | || | || | | || || | ||||||||||| |||| || ||||| || ||| | || ||||| |||||||| ||| | |||||| | |||||||| ||||| ||||||||||| || ||||
gtactgtttcctatgcagttcaaaacttatgaacgtagcatcaatagacattaaaaaagtcagatatttaggacgaatatgtcagtattcactcttactgaattaagttgatcctgataatccatttttcatcttctgaaatggagtaattttgtcttgtat-ttgtgcagGTTGCCAAGGAGAGTGCAGATGTCATAGTACTTGACGATAATTTCACAACTATAATAAATGTTGCAAGATGGGGTCGTGCAGTTTATATTAACATCCAAA
upper sequence: GLYMA09G35970.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0158g00360.t01 (Vitis vinifera), 3'ss of exon 4
--cattttatgggcatacttgatatgttttctaatcaattgattttaatattttacgtagcattgtttgttaagtattactgttaacctccatgttctccagGTTGCCAAAGAGAACGCGGATGTGATTGTAATGGATGATAACTTCACAACCATAGTGAATGTTACCAGATGGGGCCGTGCTGTTTATATTAATATACAAA
||| | | | | | | | || ||| || | | | | | || | | | | || | | || || | | ||| ||||| || ||||| || |||||||||||| ||||||||||||||||| | || |||||||||||| ||||||||||||| | || || || ||||| ||||
cattctttcttttgaaaatggtaacttcttttaaaca--tatcaaggaggtgtgccttaatacttatcatcaaccaagcatcttccccactgttatctacagGTGGCAAAAGAAAATGCGGATGTGATTATAATGGATGATAACTTCTCGACTATAGTGAATGTTGCCAGATGGGGCCGGTCAGTCTACATAAATATTCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattttacgtagcattgtttgttaagtattactgttaacctccatgttctccagGTTGCCAAAGAGAACGCGGATGTGATTGTAATGGATGATAACTTCACAACCATAGTGAATGTTACCAGATGGGGCCGTGCTGTTTATATTAATATACAAA
tgttaac putative branch site (score: 2)
cctccatgttctcc CT-rich tract
tttgttaagtatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattttatgggcatacttgatatgttttctaatcaattgattttaatattttacgtagcattgtttgttaagtattactgttaacctccatgttctccagGTTGCCAAAGAGAACGCGGATGTGATTGTAATGGATGATAACTTCACAACCATAGTGAATGTTACCAGATGGGGCCGTGCTGTTTATATTAATATACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - gcatact
- - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt