Sequence
atgc intronic sequence ATGC exonic sequencegtttttccaactgccaatattattgctcaaacatctcctcattatttcattagtttcgacattttccttactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04850.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G30360.2 (Glycine max), 3'ss of exon 13
gtttttccaactgccaatattattgctcaaacatctcctcattatttcattagtttcgacattttccttactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC
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------------gtaagtaattat-ctaatgtgatgcattggtgctatttgaattagaaaattgggattgtt--tttagttataaaaatttgtggcttcttgtaagcagGCTTGGGGTGCTTCCTCTTGAGCTCAACAAGCTGCTCATAATTGTGGTTGTATTGTCAATGGCATTAACCCCATTTCTGAATGAAGCTGGAAGAAGGGCT
upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G06890.3 (Glycine max), 3'ss of exon 12
gtttttccaactgccaatattattgctcaa-acatctcctcattatttcattagtttcgacattttccttactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC
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------------gtaagta--attatccaatatgatgcattggtgttatttgagttagaaaattgggattgtt--tttagttataaaatttgtggct-tcttgtaagcagGCTTGGGGTGCTTCCCCTTGAGCTCAACAAGCTGCTCATAATTGTTGTTGTATTGTCAATGGCATTAACCCCATTTCTGAATGAAGCTGGAAGAAGGGCT
upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 12
---------------------------gtttttccaactgccaatattattgctcaaacatctcctcattatttcattagtttcgacattttcct--tactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC
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gttggtcacaactttatcttatgcacattttttctggttaataattccatgtttcttttttcctatcaaaaaat-aataataataataattccatgtttcttttttcttaatta-gtttgtttccttcttgtatacagGCTAGGAGTGCTACCACTTGAGCTGAACAAACTTCTGATAATTGTTGTTGTGTTGTCAATGGCACTAACCCCCTTGCTCAATGAAGTTGGAAGAAGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgacattttccttactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC
tactaat putative branch site (score: 1)
ttactaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttccaactgccaatattattgctcaaacatctcctcattatttcattagtttcgacattttccttactaattaggtggtcatgattgttgcaatcatttgtgcagGCTAGGAGTGCTTCCAAATGAGCTGAACAAACTGCTCATTATCGTAGTTGTTTTGTCTATGGCATTAACACCTTATCTTAACCAACTTGGAAGAAAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA