Sequence
atgc intronic sequence ATGC exonic sequencegtgttgttatatttctctttctctattaatgaaacttcatgtaactgttaagcttttagaagacctagtccttggcaatattgctcttttttttttaacttatatatatctacttttcttctgttataaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA
Basic information
species | Glycine max |
transcript | GLYMA06G11860.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g06880.1 (Oryza sativa), 3'ss of exon 4
gtgttgttatatttctctttctctattaatgaaacttcatgtaactgttaagcttttagaagacctagtccttggcaatattgctcttttttttttaacttatatatatctacttttcttctgttataaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA
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------------------------------------gtatgttacgataatatgccaaagcaatctgtgctgtgaagcccatgataacttttctttaaca-----acaccaatttat---------tgaagGATGATGAAAGAGGCATGCGGTGGTTCTATTCTGGTGACATTGGACGTTTGCATCCAGATGGTTGCCTTGAAATTATTGACCGTAAGAAGGACATAGTCA
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgttgttatatttctctttctctattaatgaaacttcatgtaactgttaagcttttagaagacctagtccttggcaatattgctcttttttttttaacttatatatatctacttttcttctgttataaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA
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----------------------gtggcaaatcaacattat-tggtttcggcaatgttaaaagaattgg---ttggt----ttgg--ttcttcctctaaccgttttatac--acttgaatgtt----caaagGTTGATGAAAAGGGAATGAGGTGGTTCTACACAGGAGACATAGGACGATTTCACCCTGATGGCTGCCTCGAGATAATAGACCGAAAAAAGGATATCGTTA
upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv18s0001g02810.t01 (Vitis vinifera), 3'ss of exon 10
------gtgttgttatatttctctttctctattaatgaaacttcatgtaactgttaagcttttagaagacctagtccttggcaatattgctcttttttttttaacttatatatatctacttttcttctgttat-aaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA
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gtaaagctttggagattgtttatccacattctttttgtggttatatatatatagtactcttttcagaattctgacc----aaagaataattgtaaactggacatgtaataaac-tttgttaatcttttgttgttgaagGTTGATGAGAGAGGAATGAGGTGGTTTTACACCGGGGACATAGGGCAGTTTCATGCTGATGGTTGCCTTGAAATAATTGACCGTAGAAAGGACATAGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattgctcttttttttttaacttatatatatctacttttcttctgttataaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA
ttttaac putative branch site (score: 2)
tctacttttcttctgt putative PPT
tcttttttttttaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttgttatatttctctttctctattaatgaaacttcatgtaactgttaagcttttagaagacctagtccttggcaatattgctcttttttttttaacttatatatatctacttttcttctgttataaagGTTGATGAAAGAGGAATGAGGTGGTTCTACACTGGTGACATAGGGAGATTCCATAAAGATGGTTGCCTTGAGATCATTGATAGGAAAAAGGACATAGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA