Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
Basic information
species | Glycine max |
transcript | GLYMA02G00550.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
gtaaagaatatgccgagactcga-tgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
| || | | | || ||||| || || | ||| | | | ||| || | | | | | || || ||| | || || || |||||| | || | ||| |||||||||| ||||||||| ||||||||||||||||| |||||||| |||||||| ||||||||||
--------tctgttccgtccaatctatgcctttcaaaa--aaaatgttttca--agtgctaatgtcctatccttactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
gtaaagaatatgccgagactcgatgtgatcttcaactt--caacatatcctcatt----aatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
| | | | | || | || |||| ||||| | || | ||| | | | || |||| | | | | | | | |||||| | ||||| || |||||| | || | |||| |||||||||| ||| ||||||||||||||||||||| | |||||||| ||||||||||||||| |||
----------------ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtat-cagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
gtaaaga-atatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaa--acaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
||| | | |||| ||| ||| |||| | | || || || | ||| | ||| || |||| | | | | | | | || ||| |||| || || |||||| | || | |||| || ||||||| ||| ||||||||||||||||||||| | |||||||| ||||||||||||||| |||
-taataacacgtgccctgac--agactgaccttccaatctaaaat-----------tagttctgtttgattgcatccttgctgagctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
gtaaaga-atatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
||| | | |||| ||| || | | || || | || || || | | ||| | | | | || | | || ||| ||||||| || |||||| | || | |||| || ||||||| ||| ||||||||||||||||||||| | |||||||| ||||||||||||||| |||
-taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttgat-------tgcatccttgctgagctgtatccgacccacaatttttt----ttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
| | | ||| || | | || ||| | | || || | || || | | | |||| | |||| || || |||||||| | |||||||| || || |||||||| || ||||| || |||||| | || || |||||||||||||| ||||||||| |||
---------------------------gtgtgttatttc--tctagctttgttgatatgatca-gtgtcttgacatattttgaagtttttttctatgtgaatgtgtct-agATTCCAATCAAGTGGCCGAAAAGCAGAGACGAAGTTTGGAAAGTGAACATTCCTCATACTCACTTAGCGCATGAGAAGTCTGACCAAAACTGGATGGTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaaagaatatgccgagactcgatgtgatcttcaactt-caacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
||| || | | | | | | || ||| || || | ||| | ||| || | ||| | ||||| || | || ||||| |||||| | ||||||||||| ||||||||||| || || || || ||||| |||||||| |||||||||||||| ||||||||| |||
------------------------gtgtctatcgatatgttatacagttttatcgatatgattagtta-------cgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
||| | | | | | | | || ||| | | | ||| | | | || ||| | | || | | |||| | || || || | |||||||||||||| |||| |||||||| |||||||||| ||| || || ||||||||||||||| | ||||||||||| |||||||||||| |||
---------gtgct-atatttgctttcttgttttgctttgatttg---tgattggttc-ctggttacattgtcttgatattgttttgttctttgtattgatttgcgtttagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG
upper sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
|||| | | | | | || | ||| | ||| || ||| || | | ||| ||| | || |||||||| || ||||||||| | ||||||||||| || ||||||| ||| || || || |||||||||||||| ||||| ||||||||||| |||||| |||
------------------------gtgagaatgtgcgtaagctta---atagtaacaagggtgttgaagttttcttatttt-------tgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
tgctaaa putative branch site (score: 2)
tataattttgtcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcagATCCCTATTAAGTGGCCACAGAGCAGAGATGAGGTGTGGAAAGTAAATATTCCACACACTCACCTTGCACACGAGAAGTCTGACCAGAACTGGATGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT