Sequence
atgc intronic sequence ATGC exonic sequence...attgagaaataagatttgatctagttaaccctttatgacagaaataagatttgtttgacatgttatgacatatttgaacttgatgctagtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43400.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g37210.1 (Oryza sativa), 3'ss of exon 10
attgagaaataagatttgatctagttaaccctttatgacagaaataagatttgtttgacatgttatgacatatt-tgaacttgatgctagtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
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-tttacctccgtcattcagtcaggtctcctgtattttgttttctttagttgttagcaatagttactgatagggtgctgataatgttcatgtaaaatttcagTCAATACCAAATCCAGTTTTCCCTGGAGGTGCAATTATTGGATGCTCTGCAGGGTTCCTTAATGTTCCCAAAATAAAAGGAACTCATACAGCCATGAAGT
upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G032222_T03 (Zea mays), 3'ss of exon 10
attgagaaataagatttgatctagttaaccctttatgaca-gaaataagatttgtttgacatgtt---atgacatatttgaacttgatg----ctagtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
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--------ctcttctcttctcttctcttttatctatgaaatgatactcaaatcgttttttgtgttcgagaaaaaaatatgataatgatgggctcatgtaaaatttcagTCAATACCATATCCAATTTTCCCTGGAGGTGCAATTATTGGATGCTCTGCAGGATTTCTAAATGTTCCCAAAATAAAAGGAACCCATACAGCTATGAAAT
upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G03360.1 (Glycine max), 3'ss of exon 10
---attgagaaataagatttgatctagttaaccctttatgacagaaataagatttgtttgacatgttatgacatatttgaacttgatgctagtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
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ttgtttgttatcctattagtcatttgattgcctgttatttgctgcagtgcattattttctac---tcattacaaatacgaatgtgattctagttaaatttcagTCTATCCCATATCCAGTTTTTCCTGGAGGAGCAATTATTGGATGTTCAGCTGGCTTCATGAATGTGCCAAAGATAAAGGGAACTCACACGGCAATGAAAT
upper sequence: AT2G43400.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv05s0102g01110.t01 (Vitis vinifera), 3'ss of exon 10
---attgagaaataagatttgatctagttaaccctttatgacagaaataagatttgtttgacatgttatgacatatttgaacttgatgcta-gtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
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ttcatgtcttcccaaaatgtt-tcaagt---gttcatatgatttgattgtagaattttcagtattttataacaaatatgaatatgatgctaagttaaatttcagTCTATTCCATATCCAGTTTTCCCAGGTGGAGCAATCATTGGATGCTCAGCTGGCTTCCTAAACGTCCCAAAGATAAAGGGAACACATACTGCAATGAAATMapped 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|116411359|gb|EG453951.1|EG453951EST: GTACCGTGCTTCAGTATGGAGCTCGTACTTTAAATGAAGGTGGTTTTCAG TCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCT
genomic: GTACCGTGCTTCAGTATGGAGCTCGTACTTTAAATGAAGGTGGTTTTCAGgtgagttgaa ... aaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCT
EST:
gi|116411360|gb|EG453952.1|EG453952EST: GTACCGTGCTTCAGTATGGAGCTCGTACTTTAAATGAAGGTGGTTTTCAG TCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCT
genomic: GTACCGTGCTTCAGTATGGAGCTCGTACTTTAAATGAAGGTGGTTTTCAGgtgagttgaa ... aaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatttgtttgacatgttatgacatatttgaacttgatgctagtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
tagtaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgagaaataagatttgatctagttaaccctttatgacagaaataagatttgtttgacatgttatgacatatttgaacttgatgctagtaaaatttcagTCCATTCCCTATCCAGTTTTTCCTGGAGGAGCAATAATTGGATGTTCAGCTGGTTTTCTCAATGTACCCAAGATTAAGGGAACACACACTGCAATGAAAT
- - -gaaataa
- - - - - - gatttga
- - - - - - - - - - - - - - - - - - -acagaaa