Sequence
atgc intronic sequence ATGC exonic sequence...cttgccagctgattcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcctactgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04540.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G046050_T01 (Zea mays), 3'ss of exon 2
---cttgccagctgattcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcctac-tgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC-
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gtgcttgatgcttgatattggctcttaattttatgcttcagtaatgccatcagct----tattgcctttcttattgctgataacacacttcaccactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTATCTGAGAATGGGGGGTCACAGT-ATGAGCTAC
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G449163_T01 (Zea mays), 3'ss of exon 6
---cttgccagctgattcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcctac-tgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC-
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gtgcttgatgcttgatattggctcttaattttatgcttcagtaatgccatcagct----tattgcctttcttattgctgataacacacttcaccactggtttagGCTCTTGTTGAAAAGGATTGGTTAGCATTTGGTCATCCATTTGCAGAGAGAATGGGAGTTCCAACAGTAGCTGAGAATGGGGGGTCACAGT-ATGAGCTAC
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G33040.1 (Glycine max), 3'ss of exon 8
-cttgccagctg--attcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcct-actgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC-
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actagtcagctgccatttatctgttttttttatcatgtgttgaaaatgaatcaatgta----tgtgctatttaattttgcttcacttttttctcccttatgcagGCACTCGTTGATAAAGACTGGCTTGCTTTTGGTCATCCATTTTCTGATCGGGTGGGAATGCCATCTGTCTCTGGAACTGGCAATGT-GCCTTTCGAGTTAT
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G34510.1 (Glycine max), 3'ss of exon 8
--cttgccagctg--attcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcctactgttctgacttcacat-cagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC-
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cactagttagctaccatttatctgttcttttatctcatgttgaaaatgaatc-aatgca----tgtgctatttaattttgcttcatttttttctcccttatgcagGCACTCATTGATAAAGACTGGCTTGCTTTCGGTCATCCATTTTCTGATCGGGTGGGAATGCCATCTGTCTCTGGAACTGGCAATGT-GCCTTTCGAGTTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgatgcaccattgtcttatgtagtctttcctactgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC
ttctgac putative branch site (score: 2)
ttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgccagctgattcaactgcataagcagcccttataagatttttgtttgatgcaccattgtcttatgtagtctttcctactgttctgacttcacatcagGCTCTTGTCGAAAAGGATTGGTTATCATTTGGTCACCCATTTTCGGATCGGGTGGGAATGCCAAACGTGTCTGAATCTGGTAATTTTGAATTACCAATTC
- - - - - -attcaac
- - - - - - - - - - cataagc
- - - - - - - - - - - - - - - - - - - - - - tgtttga