Sequence
atgc intronic sequence ATGC exonic sequencegtaaacgaataaaagacatctcatgaatcatcttttcggtgttggattcttcatcttttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35950.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G23340.1 (Glycine max), 3'ss of exon 6
gtaaacgaataaaagacatctcatgaatcatcttttcggtgttggattcttcatcttttgatgaaaacaa-tgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
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gtatataattgaatgaattttttcttttcatacc--caatggttaagttaattggtagtcataaatttatctttgacctttattgcagAACGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCATGTTCAATATTGT
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 7
gtaaacgaataaaagacatctcatgaatcatctt-----ttcggtgttggattcttcatctt-ttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
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gtacatggttgaatg-catttcttttacttttttaaaatcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 6
gtaaacgaataaaagacatctcatgaatcatctttt-cggtgttggattcttcatcttttgatgaaaaca-atgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
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gtatataattaaatg-tatttcctttttcttttcacacaatggttaagttaattggtagtcataaatttatatttgacctttattgcagAATGTGAAGGCAGTATTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCAAAGCAAAAGAAAAAGAAGAGTAAAGCACAAAAGGCTTGTTCAATATTGT
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 7
gtaaacgaataaaagacatctcatgaatcatcttttcg--gtgttggattcttcatcttttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
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gtacatggttgaatg-tatttcttttatttttttaaaatcacgatggttaattcaatgtttttaaaaaaaaat-tggtatttattacagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCATGCTCGATATTGT
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ04304 (Selaginella moellendorffii), 3'ss of exon 6
gtaaacgaataaaagacatctcatgaatcatcttttcggtgttggattcttcatcttttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT--
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---gtccgtcttgtgacaaaggagtga--agctttttgctgctgtgttgtttgttctaaacctcttccaaaattctttgtgctccagAATGTAAAGGCAGTGTTTGATGCTGCGATCAAGGTGGTCCTCCAACCTCCAAAGCAGAAGAAAAAAAAGAAGAAG---CAAAAGGCCTGTACGATACTCTAG
upper sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ16760 (Selaginella moellendorffii), 3'ss of exon 6
gtaaacgaataaaagacatctcatgaatcatcttttcggtgttggattcttcatcttttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT---
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---gtccgtcttgtgacaaaggagtga--agctttttgctgctgtgttgtttgttctaaacctcttccaaaattctttgtgctccagAATGTAAAGGCAGTGTTTGATGCTGCGATCAAGGTGGTCCTCCAACCTCCAAAGCAGAAGAAAAAAAAGAAGAAG---CAAAAGGCCTGTACGATACTCTAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcggtgttggattcttcatcttttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
ctataac putative branch site (score: 3)
aaaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacgaataaaagacatctcatgaatcatcttttcggtgttggattcttcatcttttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC