Sequence
atgc intronic sequence ATGC exonic sequencegttagtcttcccaatataccaataacagaagtttctttttaagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G45430.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 5
gttagtcttcccaatataccaataacagaagtttctttttaagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
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-gtaaagtttctactatctactttgtattttggcacatatagtacatactaagtcatgattggatgatcccc--tttttgccaacttgcagATATGTGGGCTATGGGTGCCATAATGGCCGAGCTGTTGACACTTCATCCTCTTTTTCCTGGCACAAG
upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g02550.2 (Oryza sativa), 3'ss of exon 10
gttagtcttcccaatataccaataacagaagtttctttttaagatagtctagtgcggtgcttaacaatggttaattttaattgt------gtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
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-------------gtgagtgaagaatatttgtgcctttatgagataactatttgctctcaattacaatatgtttatttgcttatccccccgttccagATATGTGGGCGATGGGTGCCATCATCGCGGAGCTTTTTTCACTGCGACCTCTTTTCCCTGGTTCAAA
upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
--------gttagtcttcccaatataccaataacagaa-gttt--cttttta-agatagtctagtgcggtgcttaa--caatggttaatt--ttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
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gtatgaaaaataaaactaaaaaaatactatttgcttagtgtttgtctattcatggatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG
upper sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
-----------gttagtcttcccaatataccaataacagaagtttctttt--taagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
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gtatgaaaaataaaaggcttactatttgcttagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttcttcaccttg-ccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAGMapped 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|116444408|gb|EG487000.1|EG487000EST: TAGGGCACCTGAAGTACTGCTACAATCATATGTATACACGTCAAAAGTTG ATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTC
genomic: TAGGGCACCTGAAGTACTGCTACAATCATATGTATACACGTCAAAAGTTGgttagtcttc ... tgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTC
EST:
gi|116444419|gb|EG487011.1|EG487011EST: TAGGGCACCTGAAGTACTGCTACAATCATATGTATACACGTCAAAAGTTG ATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTC
genomic: TAGGGCACCTGAAGTACTGCTACAATCATATGTATACACGTCAAAAGTTGgttagtcttc ... tgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
ttttaat putative branch site (score: 3)
ttaacaatggttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcttcccaatataccaataacagaagtttctttttaagatagtctagtgcggtgcttaacaatggttaattttaattgtgtttcagATATGTGGGCGATGGGTGCTATTATGGCGGAGCTGTTGTCTCTTCGCCCTCTCTTTCCTGGAGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT