Sequence
atgc intronic sequence ATGC exonic sequencegtataagctcctcatgtgagtattgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
Basic information
species | Glycine max |
transcript | GLYMA04G05900.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g08070.3 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------gtataagctcctcatgtgagtattgaa--------tcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
| ||| | | ||| | | ||||| |||| ||||||||||||||||||||| || ||||||||||| ||||| ||||| ||||||| || ||| || |||| ||||||||||||||||| || ||
ctaattacttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagCATGCAGGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
upper sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------gtataagctcctcatgtgagtattgaa--------tcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
| ||| | | ||| | | ||||| |||| ||||||||||||||||||||| || ||||||||||| ||||| ||||| ||||||| || ||| || |||| ||||||||||||||||| || ||
cttcctaccgcattacttgaactgatttggtgattgatgaattaacagttgaatatgttttgcataataatgttgaagaaacttttcttgtagcatgcagGTCATGCTTCTCGGATTTGTGCTTCTTGGACGATCTCTTGAAGAAAGTGCCAGGCTTAAGGCTTCTAGCGATATGAATGAGCTCGTT
upper sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G21930.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------------------------------------------gta-taagctcctcatgtgagtattgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
|| ||| | || || | || ||||| |||||||||||||| ||||| |||||||| || || |||||| ||||||||| |||| | |||| ||||||| ||||||||||||||| |
gtgagtttctctagcagatccacaagaggatgaaagctttttattattacttccactacatgcaaaatacagtttcaatagtaaatttctgattgatagctcttgtcatttagtatgcagGTCATGCTGCTTGGCTTTGTGCTCCTTGGTCGTTCTTTGGAAGAAAGAGCAAAGCTTCAAGCATCTACCGATATGAATGAACTATTG
upper sequence: GLYMA04G05900.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------gta-taagctcctcatgtgagt-attgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
| ||| | ||| | | |||| | |||||| ||||||||||||||||||||||||||||| || ||||||||||| ||||| ||||| ||||| ||||||||||||||||||| |||| |
cattactcttccttgtattcattggtggcaatttctgtagatttgaaattctttcttgatgctaaatttttcaagcaggccattg--ttttttagtatgcagGTCATGCTTCTTGGTTTTGTGCTCCTTGGACGTTCTCTTGAAGAGAAGGCGAGGATCAGGGCATCTAGCGATATGAATAAACTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtataagctcctcatgtgagtattgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
tctttt CT-rich tract
tattgaatctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataagctcctcatgtgagtattgaatcttttagCATGCAGGTCATGCTTCTTGGTTTTGTGCTTCTGGGACGTTCTCTGGAAGAAAAGGCAAGGATTCAGGCATCTAGCGATATGAATGAACTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA