Sequence
atgc intronic sequence ATGC exonic sequencegttcttttcttttgtatgctttataagagattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G34430.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 3'ss of exon 2
gttcttttcttttgtatgctttataag---agattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
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gtacagtgcttgtaattgttgcatatacttaaaattggtgtttatgatggcgtctc--ttgatgaaaatggttaattgttggttt---atgcagCTCGACATTTATTCTTTGTCGAGGAAATGGAAGGAGTTAGTCGATAAGGCTCGAGCGAAGCAGCTACAGCCCCATGAATACAATTCTG
upper sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G036534_T02 (Zea mays), 3'ss of exon 3
----gttcttttcttttgtatgctttataagagattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
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gtcaaacactttaccatgcacgatgaatgctgatttttga---taattttttttaaaaataaat-------ggttacctggtggtttatg--cagCTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTG
upper sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G165176_T01 (Zea mays), 3'ss of exon 4
gttcttttcttttgtatgctttataagagattttgagt-ttactctgtattcaaaaccggtatcagtgggttgtt-ctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
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----------gtcaaacactttaccatgcacaatgagtgttgatatttttgatgattttttttaaataaatggttacttgctggtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCGCGAGCAAAGCAGTTGCAGCCCCATGAGTACAACTCTG
upper sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G31630.1 (Glycine max), 3'ss of exon 3
-------gttcttttcttttgtatgctttataagagattttgagtttactctgt--attcaaaaccggtatc---agtgggttgttctatcttttgtaaa---cagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
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gttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtagATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGATAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG
upper sequence: AT1G34430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 3'ss of exon 2
gttcttttcttttgtatgctttataagagattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
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-gtttgttaatctgttcttgctaaacttaattttggctaccctatggcttttcaagagtta--aattaattg--caatttattat----agGTGGACATTTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCCGAGCAAAGCAGCTGCAACCTCATGAATACAATACAGMapped 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|125240203|gb|EL254288.1|EL254288EST: TTGATGGTGGTTTGATCACTCCGGTGCTTCAGAACGCTGATAAG GTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGG
genomic: TTGATGGTGGTTTGATCACTCCGGTGCTTCAGAACGCTGATAAGgttcttttct ... ttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
ttgttctatctttt CT-rich tract
tattcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcttttcttttgtatgctttataagagattttgagtttactctgtattcaaaaccggtatcagtgggttgttctatcttttgtaaacagGTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG