Sequence
atgc intronic sequence ATGC exonic sequencegttgttcttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatgatgatcaattatgcagataatttccaaggttccttacttctttgttatgcctgtgtttgcagGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA
Basic information
species | Glycine max |
transcript | GLYMA09G30790.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------gttgttcttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatgatgatcaattatgcagataatt----tccaaggttccttacttctttgt-tatgcctgtgttt--gcagGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA---
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gtatgcttaaattttgctttatttcttacatgaggtagatggaactatgtttgagaacgttgaaatgtgacagtactagaggcacatagatgcagaacctagaagatgatgaaaattcaaagaacaaactgaaattctatgttccctcttaatatatgtgtgcctatatttttacagGCATTAGCTGATCCATACTTTAATGGTCTGTCAAGTAAAGTGCGGGAACCATCG---ACACAGCCGATTTCAAAGCTTGAATTTGAGTTTGAGAGAAAGAAAT
upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 7
gttgttcttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatgatgatcaattatgcagat--aatttccaaggttccttacttctttgttatgcctgtgtttgcagGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA---
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----------------gtaagtgagaagtaaa--tttgctttacttttcccttttgtt------ttatacagaacgaaactcttatattcgtcgttt--ttgattttcata---ttacagGCACTAGCTGATCCATATTTCAGTGGTTTGTCAAATTCAGAGCGTGAACCAACA---ACACAGCCAATTTCAAAGCTTGAATTTGACTTTGAGAGAAAGAAGT
upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0087g00500.t01 (Vitis vinifera), 3'ss of exon 1
----------------gttgttcttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatga-tgatcaattatgcagataatttccaaggttccttacttctttgttatgcctgtgtttgc-agGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA-------------------------------------------
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gtaccatgcgtaaaaaaaaaaccatccattcccttctcacaa----aaattccct--gatgttaatccgttggctcttcaactactggaatgtctccttgcatttgat-cctaatgatcgtccaactgttgaagaggccttagctgatccttattttgatggtttggaaaatgtagATCGTGAACCT---TCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAATTAACAAAAGATGATGTTAGGGAGTTAATATATCGAGAGAT
upper sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 6
------gttgttc-ttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatgatgatcaattatgcagataatttccaaggttccttacttctttgttatgcctgtgtttgcagGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA---
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gtaatagttggtaattctaatatttcgctacttcaa-aatttaaattaaaattgtaaagaaatataatctagttgatttgggaacactgtgcttcctaatatcattgc-gtgtttatgttggcagGCTTTAGCTGATCCGTATTTTGATGGTTTGGCAAATGTAGATCGTGAACCT---TCCACTCAACCCATTTCAAAACTTGAGTTTGAGTTTGAGAGAAGGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgcagataatttccaaggttccttacttctttgttatgcctgtgtttgcagGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA
tccttac putative branch site (score: 2)
agataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgttcttcagttacctagataaaaggggaaattttgttgaatgtgtaccaaatgatgatcaattatgcagataatttccaaggttccttacttctttgttatgcctgtgtttgcagGCACTAAGAGATCCTTATTTCCATGGTTTGTCAAATGTGGACCGTGAACCGTCGTCCACTCAGCCCATTTCAAAGCTTGAATTTGAGTTTGAGAGGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA