Sequence
atgc intronic sequence ATGC exonic sequencegtgaagttttgttttctttagtttctgatgtgagtttcattttggttctctgtatactgatgatgtgtgtcattgttctatagTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G46230.2 (Glycine max), 3'ss of exon 5
--------------------gtgaagttttgttttctttagtttctgatgtgagtttcattttggttctctgtatactgatgatgtgtgtcattgttctatagTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
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ttactgcacacatattactcgtccaataat-ttatcagtcataactaatgaatatattagtcaaactataaatttaatatggttttttctcctttttcta--gTGCTACATCAGGTGGTATTCTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTGAGGCTG
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 5
----gtgaagttttgttt--tctttagttt-----------ctgatgtgagtttcattttggttctctgtatactgatgatgtgtgtcattgttctatagTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
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acttattaattgttacttatccattaatttatcagtcataactaatgaatatattacacgaattataaatttgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------------------------------gtgaagttttgttttcttta-gtttctgatgtgagtttcat---tttgg--ttctctgtatactga--tgatgtgtgtcattgttctat-agTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
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gtaagccatgccaactatctcttgtatgtattttgatctcaattgtaaatgccatcatttagttgccattatgtgacatatccaagaagcataatatactatttgatacagataccgttgtggttcatctgtgagtattattagtatggaatgaattgtaaattgaacttttttctttctttctttcaccagTGCCACATCAGGGGGTATCTTAGACAGAGCTATTGAAGCAGAAGATAGGAAGCATGGAGATTTCCTGAGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgagtttcattttggttctctgtatactgatgatgtgtgtcattgttctatagTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
tactgat putative branch site (score: 2)
ttgttct putative PPT
tttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagttttgttttctttagtttctgatgtgagtttcattttggttctctgtatactgatgatgtgtgtcattgttctatagTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT