Sequence
atgc intronic sequence ATGC exonic sequence...gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcctaaatcgagggtgccaatgatatactacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG
Basic information
species | Glycine max |
transcript | GLYMA07G08020.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G61230.1 (Arabidopsis thaliana), 3'ss of exon 1
gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcct--aaatcgagggtgccaatgatata-ctacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
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---------------------gtatctatctatcttccttttcctccattgttccctcatgaaaaaaaaaacacaaagagaacatctttcttctccttttcagATATGTAACTACTCATCCATGGATGGAGTTTTGTATTGCAAGACCCATTTTGAACAGCTCTTCAAAGAATCTGGAAATTTCAGCAAGAATTTCCAAACAG
upper sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
gattaaattcttttcaatacaaaataagttaagattaaatt-cctttaaatattgttcctaaatcgagggtgccaatgatatactacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
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---gtatttctcttttcttcttcttcctccattgttactctgtttttcgacaatgcttc-------attgttttaaaagaccacatcttttcttaacacagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
upper sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01780.1 (Arabidopsis thaliana), 3'ss of exon 1
gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcctaaatcgagggtgccaatgatata-ctacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
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----------------------gtgcactcattactcattttcttgttagatcttctatgatcatattatatcaacaatttatctatgtgttgatgg-cagATGAGCAACTATTCCTCCATGGACGGAGTTTTGTACTGCAAGACTCATTTTGAGCAACTCTTCAAGGAATCTGGCAATTTCAGCAAAAACTTTCAACCAG
upper sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
--------------gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcctaaatcgagggtgccaatgatatactacttaatgttggt---cagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
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gtatgtttcttctaagcctatttttcccctgtttttttttttttttggt-aaatttttacgaaaatcaatatctacgtaaatttatgagatata-acaagtgggttttactttgcagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatattgttcctaaatcgagggtgccaatgatatactacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG
atatactacttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattaaattcttttcaatacaaaataagttaagattaaattcctttaaatattgttcctaaatcgagggtgccaatgatatactacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatga