Sequence
atgc intronic sequence ATGC exonic sequencegtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAGCAGCGGCAAGACATCATTGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55990.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 7
gtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAA---GCAAAAGCAAGCAGCGGCAAGACATCATTGTA
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----------------------gatttagtctggat-actttttttcttcctattt--tacttcgattgctctttggt---tactccatttcacagacctaagtacctaaccatatcaact------ttggcagGGACATCACAACTACATTTCCAAGCTTTGTCTTCCATTCTCAAGTCGACGATACTTGAAATCTGAGAATTTCCCCCTCCAATGGAATGCCAGAAGACAGT---
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
gtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAA--GCAAAAGCAAGCAGCGGCAAGACATCATTGTA
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---------------------------aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagc--taatcttgccacatg-----tgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC--
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 7
----------------------------------------------------------gtgagttccaaatctttctatttatataaccaggatt-gaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctg--cagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAG-CAGCGGCAAGACATCATTGTA
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gtaagatattctaatcttttgcgtatgctgttaactctgtttagctggaaataacaaagacaacattaaataccacgatttatttagataatatcagaacacatgcgattatcctgaatgagctagtattgtaaattgtagt-tctacttcaaccaaatcaatttatggttctaat-catgctaactttgtgcagGGACATCACCACTACATTTCCGAGCTTTGTCTTCCATTCTCAGGTCGATGATACCTGAATTTCTGAAAACTAATGAATGTCAGAAGGTGGACTGCTTGCT-
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
gtgagttccaaatctttctatttatataaccaggattgaatc-tattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAGCAGCGGCAAGACATCATTGTA
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-----------------------ctgtgagaggcaacgcatgatatgctgtcag-ttcaaagtatagatga-ctattgtcttttctt-gtgatatctcacaa-gtttgcattgctat-----atttgg---acagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGATATTCMapped 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|124815281|gb|EH900147.1|EH900147EST: GTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAA GGATATCACGACTACGTTTCCAAGCTTTG
genomic: GTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttcca ... tgctctgcagGGATATCACGACTACGTTTCCAAGCTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAGCAGCGGCAAGACATCATTGTA
cttgctct CT-rich tract
atgatatgtaataaa 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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gtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAAGCAAAAGCAAGCAGCGGCAAGACATCATTGTA
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