Sequence
atgc intronic sequence ATGC exonic sequencegtttgttatcaacatggcgtatttttttgcttttttccaatgaggtatataatcagcaatgttgttttaatggtttacccttacacattacatatatttctgtcaactgtttttccctagaaggcctaatctgtggttcttccagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01790.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 13
gtttgttatcaacatggcgtatttttttgcttttttccaatgaggtatataatcagcaatgttgttttaatggtttacccttacacattacatatatttctgtcaactgtttttccctagaaggcctaatctgtggttcttccagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT
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------------------------------gtttggccctggttctttctgtttttttgtattgttttaggtgataagatgtatatgtcacacacatctgagttaag-acaaactcatgga-----caat-----atttttgcagGGTCTTCTATCTCCTCAATTATCGTCATTATTATTTCTAGTGGTTGGCATTTCAATGGCTCTTACACCATGGTTAGCTGCTGGTGGCCAGTTTTTGGCAT
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 11
gtttgttatcaacatggcgtatttttttgcttttttccaatgaggtatataatcagcaatgttgttttaatggtttacccttacacattacatatatttctgtcaactgtttttccctagaaggcctaatctgtggttcttccagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT
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------------------------------------ttgatagagcctactgtcaagaggg--gatacagttaattttcctga-attgaatgaaaattattgtca-ttgttaggactttg-----ctaattagccttgtttgcagGGCATAATGTCTCCTCAGCTATCATCTTTGCTGTTTCTTGTGGTGGGAATTTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGT
upper sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S31_202V6.1 (Physcomitrella patens), 3'ss of exon 14
gtttgttatcaacatggcgtatttttttgcttttttccaatgaggtatataatcagcaatgttgttttaatggtttacccttacacattaca-tatatttctg-tcaactgtttttccctagaag-gcctaatctgtggttcttc--cagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT
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-----------------------------------------------tgtcatctcagctcatatctcgaggttttg---ttatgtattggaatgtgaatgggatcaacagtgatttcctggaactgaagtatctctggtttttctccagGGTATCATGAGTAATCAACTATCTTCGTTGCTCTTTCTAGTCGTGGGTCTGTCCATGGCCATCACTCCATGGTTAGCTGCTGGTGGACAGCTTCTTGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatatttctgtcaactgtttttccctagaaggcctaatctgtggttcttccagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT
gcctaat putative branch site (score: 3)
ttcttcc putative PPT
tgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttatcaacatggcgtatttttttgcttttttccaatgaggtatataatcagcaatgttgttttaatggtttacccttacacattacatatatttctgtcaactgtttttccctagaaggcctaatctgtggttcttccagGGTATAATGTCTCCTCAGTTATCTTCGTTGCTATTCCTTGTCGTGGGAATCTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG