Sequence
atgc intronic sequence ATGC exonic sequencegttctactacctgtttgcctctctctttaatgtttttacattgttattatctttatacaagataatttatggctgaacaacaatgtatgtcaagatgatcttacttgggggttattctttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG
Basic information
species | Glycine max |
transcript | GLYMA18G46780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45950.1 (Arabidopsis thaliana), 3'ss of exon 3
gttctactacctgtttgcctctctctttaatgtttttacattgttattatctttatacaagataatttatggctgaacaacaatgtat-gtcaagatgatcttact-tgggggttattctttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG
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----------------------------------------------gtttgtttgaattaga-agtaaatattttcatttccataccccgtctggcctctttcattacatctattttccactctgtagGAACGAAAAACTTATGATGAAAGATTCATCCGAATGGACACAAAGAGGCTCTGTGAGTTGACCTCTGCCGCTGACAGTTTGCAGCTGAAACCTTTGGTTG
upper sequence: GLYMA18G46780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G61415.2 (Arabidopsis thaliana), 3'ss of exon 3
gttctactacctgtttgcctctctctttaatgtttttacattgttattatctttatacaagataatttatggctgaacaacaatgtatgtcaagatgatcttacttgggggttattctt--tgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG
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-------------------------------gtttacttgaggttattaaatttg----aaacaattaatgac---atgtcgat-tatcctatgcctttttttcatagagctctttgttactttttagGAACGTAAAGTTTATGATGAAAAATTCATCCGGATGGATACAAAGAGGCTCTGTGAGTTGACCTCAGCCGCTGACAGTTTGCAGTTGAAGCCGTTGGTTG
upper sequence: GLYMA18G46780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02450.t01 (Vitis vinifera), 3'ss of exon 2
gttctactacctgtttgcctctctctttaatgtttttacattgttattatctttatacaagataatttatggctgaacaacaatg-tatgtcaagatgatcttacttgggggttattctttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG
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------------gtttgcacatatct---aacttatcattttctttttctgattagatgttcttttgctagtttgaatagcaaagctatgtt----tgacctt--ttggccatt-ttttgggcatagGAGCGGAAATCTTTTGATGAGAAGTTCATTAGAATGGATACAAAGAGGCTATGTGAGTTGACATCTGCTGCTGACAGCCTCCAATTGAAGCCTTTGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgaacaacaatgtatgtcaagatgatcttacttgggggttattctttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG
atcttac putative branch site (score: 3)
ttattcttt putative PPT
ttattctttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctactacctgtttgcctctctctttaatgtttttacattgttattatctttatacaagataatttatggctgaacaacaatgtatgtcaagatgatcttacttgggggttattctttgtatagGAACGAAAGTCTTATGATGAGAAATTCATTAGGATGGACACAAAGCGGCTATGTGAGTTGACATCTGCTGCAGACAGCCTTCAGTTGAAGCCATTGGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC