Sequence
atgc intronic sequence ATGC exonic sequencegtatttaaggacataatgatgcttcacactttcacttcattctatatagttttcatttatgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
Basic information
species | Glycine max |
transcript | GLYMA04G37780.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
---gtat-ttaaggacataatgatgcttcacactttcacttcattctatat---agttttcattt----atgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
| | || || | || || | ||| | ||| |||| | | ||||| ||| | | | || | | | ||| || |||| || | |||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||| ||||||| |||||||||||||| || |||||| | |
gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gtatttaaggacataatgatgcttcacactttcacttcattctatatagttttcatttatgagtcctatttactg--atctctccatctgcac-tacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
| |||| || |||| || | ||||| | | ||| | |||| || || | | || || |||| || | |||||| ||||| || || || ||| | || ||||| ||||| | ||| ||||| ||||||| |||||| ||||||||||| |||||||| |
---------------gtaccacttcctggtt-cactaggaatta---aagcttcatgcagacattctagt-actgtcattcctgaaacaaagtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatttaaggacataa-tgatgc-ttcacactttcacttca---ttctatatagttttcatttatgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
|||||| ||| | || || | ||| | | ||| | || | | || || | | | || | |||| | || | || ||||||| | || ||||||| ||||| || ||||| |||||||| ||||| ||||||||||| ||||| | ||| | |||||||| || || ||||| |
----gtaaggaaatatcttttgtattgaggcttactcgtcaaactgctgtcacatctttatactctcttgttttatatttatctgttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------gtatttaaggacataatgatgcttcacactttcacttcattctatatagttttcatttatgagtcctatttact--gatctctccatct------gcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
| | || ||| | || || | ||| ||| | || ||| ||| | || |||| | | || | | | || |||||| | ||||||||| ||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| |||||||||||||| || || ||| | |
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttc-ctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcacta-gtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
upper sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S249_58V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------gtatttaaggacataatgatgcttcacactttcacttcattctatatagttttcatttatgagtcctatttactgatctctccat------ctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
| | || | || | ||||| | ||| | || | | || | | | ||||||| |||| | || || ||| | ||| | |||| ||| |||||||| ||| || || |||||||||||||| |||||||||||| |||||| |||||| || |||||| | |||||| | |
gtaggaatttgagctgaggaattctaaatatgtagttgcttacgatacgggcttaaagctgaaaacgcagacctttttatccttatttacatatctgtttatttttttcttttttacttatagATACAAACCATCAAGCAAGGATACATTTTGAAGCGTTCCTCAAATTTGAGAGGTGACTGGAAGCGAAGGTTTTTTGTGCTGGATAGTAGGGGAATGTTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagttttcatttatgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
tactgat putative branch site (score: 2)
tttcatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttaaggacataatgatgcttcacactttcacttcattctatatagttttcatttatgagtcctatttactgatctctccatctgcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA