Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgctgtttgtgttgtcttctgtctttcatagcttaacatttcatttatcccatacttctgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTGTGGGCAAGGAAACTATGGATTTACTGATTACAGAGACTGGTATTGGAGCTGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G15860.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G15860.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G01190.1 (Glycine max), 3'ss of exon 6
-----------------------------------gtttgtgctgtttgtgttgtcttctgtctttcatagcttaacattt-----catttatcccatacttctgat-cttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTGTGGGCAAGGAAACTATGGATTTACTGATTACAGAGACTGGTATTGGAGCTGAGA
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gtgctaatgcatcttctctattagaggtttggaaaatttgtcattctttgattgatattcattatcaataattacagatatacatgcatatttcttctattcattgtgctgcagACAGGAAAAGCTTTTACTGCAAAGGGAATGCAAGTTCTTGAATATGTTGGTAAGGAGACAATGGACTTATTAATCAGTGAAACTGGAATTGAGGTTGAGA
upper sequence: AT2G15860.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G29660.1 (Glycine max), 3'ss of exon 4
---------gtttgtgctgtttgtgttgtcttctgtctttcatagcttaacat-----ttcatttatcccatactt-ctgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTGTGGGCAAGGAAACTATGGATTTACTGATTACAGAGACTGGTATTGGAGCTGAGA
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gtttggaaaaattgtcattcttcatttgatattcattatcagtaattacaaatatacatgcatatttcttctattcattgtgctacagACAGGAAAAGCTTTTACTGCAAAGGGAATGCAAGTGCTTGAATATGTTGGTAAGGAGACAATGGACTTATTAATCAGTGAAACTGGAATTGAAGTTGAGA
upper sequence: AT2G15860.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv03s0063g01360.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtgctgtttgtgttgtcttctgtctttcatagcttaacatttcatttatcccatacttctgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTGTGGGCAAGGAAACTATGGATTTACTGATTACAGAGACTGGTATTGGAGCTGAGA
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gtttg-gttggcactcatctttttgtttattaattttgagacacttc-cttatttcttgcttttg--ttacagACTGGAAAAGCTTTTACTGCAAAGGGAATGCAAGTGCTGGAGCTTGTTGGTAAGGAGACCATGGACTTACTGATCACAGAGACTGGTATTGAAATTGAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164094512|gb|EL995144.1|EL995144EST: AGGTTCTTCGCCTAGGGAAGCTTGGATCTGGTGCACCGTCTCTACTAGAA ACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTG
genomic: AGGTTCTTCGCCTAGGGAAGC-TGGATCTGGTGCACCGTCTCTACTAGAGgtttgtgctg ... tgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTG
EST:
gi|164028735|gb|ES122774.1|ES122774EST: AAGGTTCTTCGCCTAGGGAAGCTGGATCTGGTGCACCGTCTCTACTAGAA ACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTG
genomic: AAGGTTCTTCGCCTAGGGAAGCTGGATCTGGTGCACCGTCTCTACTAGAGgtttgtgctg ... tgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttctgtctttcatagcttaacatttcatttatcccatacttctgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTGTGGGCAAGGAAACTATGGATTTACTGATTACAGAGACTGGTATTGGAGCTGAGA
ttctgat putative branch site (score: 3)
tacttct CT-rich tract
ttaacatttcatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgctgtttgtgttgtcttctgtctttcatagcttaacatttcatttatcccatacttctgatcttcagACAGGAAAAGCATTAACTGCGAAAGGAATGCAAGTACTTGAATTTGTGGGCAAGGAAACTATGGATTTACTGATTACAGAGACTGGTATTGGAGCTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA