Sequence
atgc intronic sequence ATGC exonic sequenceGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53170.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 5'ss of exon 3
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttc----attttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa-
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GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCATgtaagtaactgagtaaatatttgttactcttctca--tgtactatca--gcagttcatatttattgtaatattccatattaatttatttgtttgagctgctttag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G004040_T01 (Zea mays), 5'ss of exon 11
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttc-------attttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaa------ctgatacctttttcttgtcttgagaa-
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GGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCATgtaagtcgtctgagcatatgttttcctgatcttgatgaagtgtatcacc--taaaagttctatccagtg-agtgcaaaaaagtttgattaattctgttgagctttctttactag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G156069_T01 (Zea mays), 5'ss of exon 11
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtatta---gtattgcagataagagttactggaa--tacgaagaactgatacctttttcttgtcttgagaa-
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GGAATAATTGTGATGGCTGCAACAAACTTGGCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCATgtaagtcacctgagcatatacggtttcctgatcttgatgaagtgtatcacctatcaagtgcagtgcaaattttttttgattaattccgttgagctttcttcactag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA06G13140.1 (Glycine max), 5'ss of exon 11
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa--------
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GGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACATgtaagcccta---ttcctttttctcctcgataacagaat----ttataaagagaaaataggaggataagaaatccttctagaacaa-caaaagaagaaaataaactag
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA14G29810.1 (Glycine max), 5'ss of exon 3
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa-
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GGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCATgtaagtcctattttttttccccaacagatgaatc-tattaagagaaataatataaatagaaagaatgatgattgtaagtcttaatctataatactgttgta
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA13G08160.1 (Glycine max), 5'ss of exon 11
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaac--tgatacctttttcttgtcttgagaa
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GGAATAATATTAATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACGAGGCCTGGCAGATTTGATCGGCATgtaagtcctatttatttttcccaatagatgaaatg-atgaat-ctattaagggaaataatataaatagaaagaatgattatggttagtcttaatctacaata
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 5'ss of exon 11
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattct--tctgagacgtatt----agtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa
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GGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCATgtaagttattttctctgtatgataatagtttgatacttttttcaaagtcttgaagcttgaaactgttc-attatgaataatt--tatcctatactgaagatga---
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S9_238V6.1 (Physcomitrella patens), 5'ss of exon 11
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa--
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GGCATCATTGTGCTAGCAGCTACAAATCTCCCCGAGACTCTTGACCCAGCTCTGACACGACCTGGTAGATTTGATAGACATgtaagtatgt-tggtcctatcaatttcttggtaaacatta-caggacagtctatccttgcacatttggtgattgtttttgtgcgttatatatatatatatatMapped 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|125257414|gb|EL271499.1|EL271499EST: TACTTGATCCAGCTCTGACAAGACCGGGTGGATTTGATAGACAT ATTGTCGTACCCAGTCCGGATGTCCGTGGACGCGAAGAGATTTTGGAACTC
genomic: TACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttc ... ttgattttagATTGTCGTACCCAGTCCGGATGTCCGTGGACGCGAAGAGATTTTGGAACTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACATgtaagttttcattttcttgttattcttctgagacgtattagtattgcagataagagttactggaatacgaagaactgatacctttttcttgtcttgagaa
- - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttttct