Sequence
atgc intronic sequence ATGC exonic sequencegttagtttttatcaactgctcacacaaactccccttgattgctgttcatatctctttctcggattgctgcctaaaacaacatgactcattcctctatttcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
Basic information
species | Glycine max |
transcript | GLYMA13G40080.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 2
----------------------gttagtttttatcaactgctcac---acaaactccccttgattgctgtt-catatctctttctcggattgctgcctaaaacaacatgactcattcctctatt---tcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
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gtattttcttttcttttataaaaagaagaacaaccacttatgcacaaaacaaacgaccctttgccaccctcacttaatgcattctctttcccct-tcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 2
--------gttagtttttatcaactgctcacacaaactccccttg-attgctgttcatatctctttctcggattgctgcctaaaacaacatgactcattcctctatttcttgt----ttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
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gtttagacatttcttcatattgaatcgtcagctagagaatggttgtattgtggggtttatcgttttaacttttaactgatttactctcgttgcatttcgtttttaatcgttgtatcgtttagATATGGAGATGAACATAAGCTTGCTGGATTTTCAGCTACTCTTCAAGCTATTATTTCTTTTGTGGAGAATGG
upper sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g02820.t01 (Vitis vinifera), 3'ss of exon 2
gttagtttttatcaactgctcacacaaactccccttgattgctgttcatatctctttctcggattgctgcctaaaacaacatgactcattcctctatttcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
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--aaagtcaacttaagtaattaagtaataattattaagttttaccaaatgcccactt----agtctctgtttaacttt---tgtttcttttttcttttattacatcaagATATGGAGATGAGCACAAGCTCGCAGGATTCTCAGCAACATTGCAAGCTATCATTTCGTTTGTGGAGAATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctcggattgctgcctaaaacaacatgactcattcctctatttcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
gcctaaa putative branch site (score: 3)
ctcattcctctatttc putative PPT
taaaacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttttatcaactgctcacacaaactccccttgattgctgttcatatctctttctcggattgctgcctaaaacaacatgactcattcctctatttcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA