Sequence
atgc intronic sequence ATGC exonic sequencegtatcatatttctttggctggtaagtaacatacaattttaattgggcaatgcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
Basic information
species | Glycine max |
transcript | GLYMA20G08360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g04020.2 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------gtatcatatttctttggctggtaagtaacatacaattttaattgggcaatg--cagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
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gtcagtcttctctatttacctttataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG----------
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------gtatcatatttctttggctggtaagtaacatacaattttaattgggcaat--gcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
||| |||| | | | | | | | ||| | ||| || | | | |||| ||||| ||||||||||||||||| ||| |||| || | ||||||||||| || | |||||| ||| |||||||||||
ataactaaataagtgaaaatggccgctgatgaagtatagtgatcgtaatgtattaccacaagttactccttttctcaattgatgattaactggttttcagGTTTTATGGGACCTTCCAAGGTTTGTGAAGATAGTTGAAGTTGGACCACGGGACGGTCTGCAAAATGAGAAGAATACTGTACCCACATCTGTAAAGATTG----------
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G26800.3 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------------------------------------------------------------gtatcatatttctttggctggtaagtaacatacaattttaattgggcaatgcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
| ||| ||| ||| || || | | ||| || || ||| || | |||||||||||||| ||||| ||||| || |||||||||||||| ||||| | || ||||||||||| || ||||| ||| ||||||| | |
gtaattgtctcgatggaggaaagtagtttttgacctctatataaaacatatccacagatacctcgttccccgtctatgtaggatagttttgtataatgattcatctttttcatttctgtttaaaatttcccactacaaccaccatttttttttctctctta--ttctgttttttttctgtttgg-aatttagATCTCTAAAGGTATACCAAAGTTTGTGAAGATTGTAGAAGTTGGTCCAAGAGATGGCCTGCAGAATGAGAAAAATATAGTACCCACATCTGTAAAGGTGG----------
upper sequence: GLYMA20G08360.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------gtatcatatttctttggctggtaagtaacatacaattttaattgggcaat-gcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
|| |||| | || | | | || || || || | || ||||||| | |||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||| || |||||||| |||| |||||| | |
taataatataattttgcattttacaatctttgtgttactggagttgtttcatctgatttattttattttatgttttatttttgtactttgataagagcagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG---------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctttggctggtaagtaacatacaattttaattgggcaatgcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
taagtaacatacaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcatatttctttggctggtaagtaacatacaattttaattgggcaatgcagtttatgaaagGTATACCAAACTTTGTAAAGATAGTTGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAAAACATTGTACCAACAGATGTAAAGATTGAATTGATTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG