Sequence
atgc intronic sequence ATGC exonic sequencegtaatctttcagtttcaaatatatttgccattccttttacggtgaacatggatagagaaattttcagttaagctaaagggaaataaaatgcatgcaaaaacttagaaaaatgtaacattcagaacttggttcaaagtgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA
Basic information
species | Glycine max |
transcript | GLYMA20G26800.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G26800.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0091g00540.t01 (Vitis vinifera), 3'ss of exon 7
gtaatctttcagtttcaaatatatttgccattccttttacggtgaacatggatagagaaattttcagttaagctaaagggaaataaaatgcatgcaaaaacttagaaaaatgtaacattcagaacttggttcaaagtgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA
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--------------------------------------------------------------------------------------aat-cagactgccatttggggctgaattccagtggcagctt---ttgatgttct-gtttttgtaggattctttcttatctttcaatgtgctgagctttattgcagACATCTATGCATGGAAGCTGTCCAGTGATTGAAGGGGAGAAGTGGGTGGCTACAAAGTGGATCAGAGATGAACAACAAGAAGACTAA------------
upper sequence: GLYMA20G26800.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S172_91V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaatctttcagtttcaaatatatttgccattccttttacggtgaacatggatagagaaattttcagttaagctaaagggaaataaaatgcatgcaaaaacttagaaaaatgtaacattcagaacttggttcaaagtgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA-
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------------------------------------------------------------------------------------attatttct-taacaccctccttacatcagttgtttgtgctttggttatgcttggcgatgaacgtg-caaaccttcttgttctaatgtcttcccaaca-----acagACCGCATTGCATGGAAGCTGTCCAGTTATCAAAGGCGAAAAATGGGTCGCCACGAAGTGGATACGCAATACCGACAAATTTTAATCTGAAAGATCCCACT
upper sequence: GLYMA20G26800.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15913 (Selaginella moellendorffii), 3'ss of exon 7
gtaatctttcagtttcaaatatatttgccattccttttacggtgaacatggatagagaaattttcagttaagctaaagggaaataaaatgcatgcaaaaacttagaaaaatgtaacattcagaacttggttcaaagtgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA
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--------------------------------------------------------------------------------------------------------------------------------------gtcagtcgatcgaaaacgaagaaatcgccactgacatattg-tcgccgttgtt--agACTGCATTGCACGGGAGCTGTCCAGTGATTAAAGGCGAGAAATGGGTCGCCACAAAGTGGATCAGGGACAAAGAAGATTGGT-CTTGA-----------
upper sequence: GLYMA20G26800.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ33274 (Selaginella moellendorffii), 3'ss of exon 6
gtaatctttcagtttcaaatatatttgccattccttttacggtgaacatggatagagaaattttcagttaagctaaagggaaataaaatgcatgcaaaaacttagaaaaatgtaacattcagaacttggttcaaagtgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA
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--------------------------------------------------------------------------------------------------------------------------------------gtcagtcgatcgaaaacgaagaaatcgccactgatatattg-tcgccgttgtt--agACTGCATTGCACGGGAGCTGTCCAGTGATTAAAGGCGAGAAATGGGTCGCCACGAAGTGGATCAGGGACAAAGAAGATTGGT-CTTGA----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA
acttaat putative branch site (score: 4)
tatttct CT-rich tract
acttaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctttcagtttcaaatatatttgccattccttttacggtgaacatggatagagaaattttcagttaagctaaagggaaataaaatgcatgcaaaaacttagaaaaatgtaacattcagaacttggttcaaagtgatcatttttggaacaagtcattttgtttgtcaccccacttaatatttctgcagACTTCTCTTCATGGAAGTTGTCCAGTGATTAAGGGGGAGAAATGGGTCGCAACGAAGTGGATTGATGATAGAGAGCAACACCACTTGCTTTCTTTATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA