Sequence
atgc intronic sequence ATGC exonic sequencegtaatatattttaaactttttgttgtcgttttattttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
Basic information
species | Glycine max |
transcript | GLYMA02G44610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
--------------------------gtaatatattttaaactttttgttgtcgttttatt-ttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
| ||| | ||| | | || | ||| | |||| | | || | | | ||| ||| | || | || ||| | | | ||| | | | |||| |||||| |||||||| |||||||| ||| |||| || | |||||||||||||| | |||||| || ||||||||||||
gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattacc-acaagttactccttttctcaattga--tgattaactggtt--ttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG-----------
upper sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 3
---gtaatatattttaaactttttgttgtcgttttatttt-atcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
| ||| | ||| | | || | ||| | |||| | | || | | | ||| ||| | || | || ||| | | | ||| | | | |||| |||||| |||||||| |||||||| ||| |||| || | |||||||||||||| | |||||| || ||||||||||||
ataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattacc-acaagttactccttttctcaattga--tgattaactggtt--ttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG-----------
upper sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 3
--gtaatatattttaaactttttgttgtcgttttatt-ttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
||| | ||| | | | || | | | || | | || || | ||||| | ||||| || || | |||| | | | ||| | || | |||| |||||| |||||||| ||||| || ||| ||||||| | ||||||||||||| | |||||| || ||||||||||||
taactgaataagtgaaaatggtggctgaaaaagtgtagtgattgtaaaatatta-ctacaaattactcttttttctcaattgat-gaataactggtt--ttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGGGATGGTCTGCAAAATGAGAAGAGTACTGTACCAGCTTCTGTAAAGATTG-----------
upper sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------------gtaatata-ttttaaactttttgttgtcgtttt-attt---tatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatg------atgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
||| ||| |||| | | | || |||| |||| | | |||||| | | | | ||||| | ||| | | | | || || || || |||||||||||||||| ||||| ||||||||||||||||| ||||| | || |||||||| || || ||||| || |||||||| | |
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctcttattctgttttttttctgtttggaatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG-----------
upper sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
--gtaatatattttaaactttttgttgtcgttttattttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgat-gcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
||||||| ||| | |||| || ||| | ||| | | || ||| | | ||| |||||| ||||| || || | || | ||||| | | |||||||||||||||| |||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||||| | |
taataatataattttg-cattttacaatc--tttgtgttactggagttg-tttcatctgatttattttattttatgttttatttttgtactttgataagagcagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
acatattttcaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatattttaaactttttgttgtcgttttattttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC