Sequence
atgc intronic sequence ATGC exonic sequencegtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G29900.1 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
gtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttt-taattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
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-------------------------------------------------------------------------------------------------------------gttagggaagttggagct--taataatcttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttc-tagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG
upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
gtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaatta-gatatccattttaataatcgtctcat-tcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
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--------------------------------------------------------------------------------------------------gtttg-gcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
gtttgta-tccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
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gttagtactactttgagat-----attttaatttgttctg--------ttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcatt---gaatatttgaagcacaactgat--gatgacaattgtttttctc----catggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG
upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
gtttgta-tccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
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gtttgtactactttgagat-----atttttatttgtt----------ctgttttttgccattagta-gtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatat----tgaagcacaactgat--gatgacaattgtgtttctc----catggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG
upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 28
gtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcc-tatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
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---------------------------------------------------------------------------------------cgagtttgttgatcaaagtttcccttcgatgcctacagc-atttg-gataagttgaagaagctgggatctt-tgtaactgttgat--ttctcttgttgcatttagGTTGTCAGATGGGGACGATCTGTATATGCAAATATACAGAAATTCATCCAGTTTCAGCTCACAGTTAATGTTGCAGCTCTAATAATTAATGTCGTGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
ttttaat putative branch site (score: 3)
tctcattcct putative PPT
aattagatatccattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG