Sequence
atgc intronic sequence ATGC exonic sequence...taattaataaagaaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatctcagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT
Basic information
species | Glycine max |
transcript | GLYMA13G07020.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G07020.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
--taattaataaagaaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatctcagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT
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catagcta-tagctaagcttgg-ataataattcttgacagaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC
upper sequence: GLYMA13G07020.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G052606_T01 (Zea mays), 3'ss of exon 1
taattaataaagaaccatgatacaaggtatatgtattgaaatatgtgttgttt-ccatttgttttctcttcttttaac---catttccaagttgtaaatctcagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAAC--AACAAT
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--gtacgtacgtacgcatgacactttctctctg-acagaaagatcctggatcgatcgtttgcttactgtgaaatcaaccctcacttgcgacat-tatattccagGTGGTCTCAGATTGCTGCCCGGTTGCCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGGCTCAAGAACAGCTCGGCA--
upper sequence: GLYMA13G07020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G12870.1 (Arabidopsis thaliana), 3'ss of exon 1
taattaataaagaaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatctca--gATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT
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ggatcactctctaattcccatgcaaacca--tgcactggtatacattttacataacatcatctcattaaactattctactctcttattcttcgatttcatagGTGGTCTCAGATTGCAGCACGATTGCCTGGTCGGACCGATAACGAGATCAAGAATTTCTGGAACTCAACAATAAAGAAAAGGCTAAAGAAGATGTCCGAT
upper sequence: GLYMA13G07020.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
--taattaataaag--aaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatct-cagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT-
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gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacat-tgttatt----tttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCA-GCATGGGAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatctcagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT
ttttaac putative branch site (score: 2)
atttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattaataaagaaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatctcagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - ataaagaa
- - - - - - - ccatgat
- - - - - - - - - - - - - - - - - - - - - -tgtgttg