Sequence
atgc intronic sequence ATGC exonic sequencegtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
Basic information
species | Glycine max |
transcript | GLYMA01G40380.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
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--------------------------------------------gtaagtac---acacttcaatcttcatggattcatgatttccccctcaaattt--ctcgggaaaataatgatggattttgact---tctttatttttgtttgattaaa-tctttatta--gGAGGTTATGATATGGAGGAGAAAGCTGCTCGAGCATATGATCTTGCTGCACTCAAGTACTGGGGTCCCTCTACTCACACCAATTTCTCT
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
|| | || | || || ||| | ||| || | || | | | | ||| || || |||| || | | ||| ||||||||||||| |||||||||||||| ||||||||||||||| |||| ||||| |||||||||||||| || | ||||| ||||||||
---------------------------------------------------------------tttcagtttatcttggtaagccttcttatagagaggttcaacatttaatcatac--accccattcaatttttcatcatctcatgtcctgaaactgattttagGGGGTTATGACATGGAAGAAAAAGCTGCAAGAGCTTATGATCTGGCAGCACTTAAGTATTGGGGACCTTCTACCCATATCAATTTCCCG
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 3
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
| | || || || | | | | | || | || | | ||| | | | | | |||| | || | | | | |||||||||||| | ||||| |||||||| |||| |||||| |||| || ||||||||||||||||| | | || || || ||
-------------------------------------------------------aatgcgcagtttacctg--ggtgagtgtcactctttgttgttcgtgcttgaagttttttttcgttcctcatttaatgtt--------tcttgccgggaatgaatgcgcagGGGGTTATGACAAAGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT
upper sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 3
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
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------------------------------------------------------aatgcgcagtttacctgggtg-----agtgtcactc--tttgttgttcgtgcttgaagt----gttttttcgttcctcatttaatgtttcttgccgggaatgaatgcgcagGGGGTTATGACAAGGAAGAGAAAGCAGCGCGAGCGTATGATCTGGCGGCGCTCAAGTATTGGGGACCTACGACCACCATCAACTTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
tttttatt CT-rich tract
acaagtcatttcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattttccaaatccaggattagttttctttttaattttgttcaaattccttgaggatagattaacttgaagttaaaaatatcatttaatattttgctcatgatgatagcaaaagaaaaaaaataaatgcttgcacaagtcatttcaaaatttttattatagGGGGTTATGATATGGAAGAAAAAGCAGCAAGAGCTTATGATATGGCCGCACTCAAGTATTGGGGACCCTCCTCTCATATAAATTTCCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC