Sequence
atgc intronic sequence ATGC exonic sequence...gtttggtatttatgataaactatgttttctgactttatttgttcgagctattgtgctaatgtccctacgttaaatggccaatactatttttctttctcagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
Basic information
species | Glycine max |
transcript | GLYMA12G07340.4 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g50330.1 (Oryza sativa), 3'ss of exon 5
--gtttggtatttatgataaactatgttttctgactttatttgttcgagctattgtgctaatgtccctacgttaaatggccaatactatttttctt--tctcagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
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caataaaataactggaataaactttgcttgcttaaagaatctctatgtactgtt----taacgtctcaattatctgacagcatcaccttttgtattggtgacagGTATCCATCATGAAAATGTTGGATCATCCTAATATAGTAAATCTCATTGAAGTGATTGATGACCCAAATGCAGATAAATTCTACATGG
upper sequence: GLYMA12G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G057084_T04 (Zea mays), 3'ss of exon 6
------gtttggtatttatgataaactatgttttctgactttatttgttcgagctattgtgctaatgtccctacgttaaatggccaatactatttttctttct----cagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
||| || | | ||| | ||||||| |||| |||| | | |||| | ||| | | ||| | ||||| || | ||||| ||| |||||||||||| | || ||||| || |||||||| |||| ||||||||||||||| | | || || ||||||||||
atcctgattttacatat-taatagggtgcattttctg-------ttgtgtacagtatttaattgcttgccctccttta--ttgttcatatttttttttcttttgagacagGTGTCCATAATGAAAATGCTGAATCACCCTAACATTGTCAATCTTGTTGAAGTGATTGATGACCCAAACATAGATAAATTCTACATGG
upper sequence: GLYMA12G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G60550.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttggtatttatgataaactatgttttctga-ctttatttgttcgagctattgtgctaatgtccctacgttaaatggccaatactatttttctttctcagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
|||| | | | || |||| | |||| | | | | | || | || ||| | || || | | | |||||| | ||||||||||| |||| |||||||| || || || |||||||||||||| |||||||| || || || | || |||||||
-----gtatccttagtttttttgcattgctgaacagcatttctattggtt-tcattttagagaagttatgtttat--gctcatttatcctataacttacagGTTATGATTATGAAAATTTTGGAGCATCCTAACATCGTTAACCTCATTGAGGTGATAGATGACCCTGAAACTGATCATTTTTACATGG
upper sequence: GLYMA12G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G45240.3 (Arabidopsis thaliana), 3'ss of exon 6
-----gtttggtatttatgataaactatgttttctgactttatttgttcgagctattgtgctaat-gtccctacgtt-----------aaatggccaatactatttttctttctca--------gGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
||| | | | ||||| | | | || || ||| || || ||| || | | || ||| || | | | ||||| | ||||| |||| | |||||||||| ||||| ||||||||||| || |||||||||||||||||||||||||| ||| || | || |||||||
gtatcatttctgaacaacatttaacta-acgtcccaagttggctttttccag-tacaatgcagatagactttaggtttcatttcagaaaacttatgtacatgttttttgtatctcatcgttgtagGTTATGATTATGAAAACCCTGGAGCATCCTAATATCGTTAATCTCATTGAGGTGATTGATGACCCTGAGTTTGATGATTTTTACATGG
upper sequence: GLYMA12G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g02990.t01 (Vitis vinifera), 3'ss of exon 6
-----gtttggtatttatgataaactatgttttctgactttatttgttcgagctattgtgctaatgtccctacgttaaatggccaatactatttttctttctcagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
|| || | | | | || | ||| | | || | | | | ||| | | || | ||| ||| || ||||| | || ||||||||| || | ||||| |||||||||||||||||||||||||||||||||||| || || ||||||| ||||
gtttttcttcgtttattgggtgaatgacactttttaatgacatcatcaacaagttctaccttgatgaaggt---tcaatttattcatatcctttgcgttgt--agGTTTTGATCATGAAAATGTTGAACCATCCAAATATAGTCAATCTCATTGAGGTGATTGATGACCCAAGCACAGATCACTTCTATATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agctattgtgctaatgtccctacgttaaatggccaatactatttttctttctcagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
tgctaat putative branch site (score: 2)
tactatttttctttct putative PPT
aatactatttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggtatttatgataaactatgttttctgactttatttgttcgagctattgtgctaatgtccctacgttaaatggccaatactatttttctttctcagGTTCTCATTATGAAAATGCTGGAACATCCTAATATAGTCAATCTCATTGAGGTGATTGATGACCCAGAGACGGACAACTTCTACATGG
- - - - - - -gataaac
- - - - - - - - - - - - - ttctgac
- - - - - - - - - - - - - - - - - - - - - - - gctattg