Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttttttcacaaatggtgaatcaagattcaagatttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18500.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g21960.1 (Oryza sativa), 3'ss of exon 2
--------------------------gtaagtttttt-ttcacaaatggtgaatcaagattc-aagatttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
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gtaagtcttgccctgcttatcagagtttgatctttttgtttattctccttgtctcttgtctccaataccacaaatcagacagctttaagtttttcca-atcgatgttttgtaaacttgcagAGGACAGGCCGAGAAGGAATTCAGAGTTGAAGTTGAGGCTATTGGTCATGTTCGCCACAAGAACTTGGTCCGGCTTCTGGGTTACTGTGTGGAGGGTACT
upper sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g01740.2 (Oryza sativa), 3'ss of exon 4
---------gtaagttttttttcacaaa-------tggtgaatcaa----gattcaagatttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
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gtgagtatttttcgttttttcttataacaattctttggtgatgcagtggcagtgcattggttagtttgttgtccttccttttacttaagctatgac-cacttgccttgggcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
upper sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g01740.1 (Oryza sativa), 3'ss of exon 4
---------gtaagttttttttcacaaa-------tggtgaatcaa----gattcaagatttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
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gtgagtattttccattttttcttataacaattctttggtgatgcagtggcagtgcatgggtcagtttgttgtccttccttttacttaagctatgac-tacttgccctgtgcagAGGACAAGCTGAGAGAGAATTCAGAGTGGAAGTTGAAGCAATTGGTCATGTCCGACACAAGAATTTGGTTCGCCTTTTGGGGTACTGTGTTGAAGGCACT
upper sequence: AT5G18500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G034855_T02 (Zea mays), 3'ss of exon 2
gtaagttttttttcacaaatggtgaatcaagattcaagatttcatttcttgaatccttttttcttttaat-------ggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
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gtaagccttccttatctaatctcagctcgttatttacctgcttgtcttccttaccaatgttgcatttagtttctccaattgatgttttgtgaatctgtagAGGTCAAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCMapped 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|124817338|gb|EH902204.1|EH902204EST: ACCTTGTTAATGGTACTCCTGTTGCTGTTAAAAAGTTTGCTCAACAATTT AGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGT
genomic: ACCTTGTTAATGGTACTCCTGTTGCTGTTAAAAAG-TTGCTCAACAATTTgtaagttttt ... tatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
ttttaat putative branch site (score: 3)
tttttgtatttctt putative PPT
ttttttcttttaat 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
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gtaagttttttttcacaaatggtgaatcaagattcaagatttcatttcttgaatccttttttcttttaatggtgatgtttttgtatttcttagAGGACAAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA