Sequence
atgc intronic sequence ATGC exonic sequenceCGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G13730.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGC-------Agtaagtacttgtccttgctaatgtaccatttttttcttattttattt-gtacacatattgttctacctcttttagttctttt--tgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagtta-tgcag
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TGCAAAGCTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGTTTCGGAATGATCCAGATGATAAAAATGCTgtatggagtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgatt---ttattttgctatccggaatccctacag
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g68010.3 (Oryza sativa), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGC-------Agtaagtacttgtccttgctaatgtaccatttttttcttattttatttgta-cacatattgttctacctcttttagttctttt--tgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagtta-tgcag
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-------CTGAATGCCGGAATACGTTATGTACAAGGGATGAATGAAATTTTGGCACCTCTCTTCTTTGTGTTTCGGAATGATCCAGATGATAAAAATGCTGTATGGAgtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgatt---ttattttgctatccggaatccctacag
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G022308_T02 (Zea mays), 5'ss of exon 7
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagt--acttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
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TGCAAAATTGAATCCGGGTATAAGATATGTACAAGGAATGAATGAGGTTTTGGCACCTCTCTATTATGTTTTCAAGAATGACCCTGACCAAAGTCAAGCTgtaagtccacttattctgattattctgagagtacaaac-------atttatg-acattaaatttctgtgaacgtagca-tgtatgggtaaataatgataaatgatatgc---------------------------------
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G068392_T01 (Zea mays), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtactt-gtccttgctaatgt-accatttttttcttattttat-ttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttat-gcag
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TGCCAAGCTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTgtatggagtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagt-----cattactatatcttctgtatcg--tgatcttgctattcggaacccttgtag
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G068392_T03 (Zea mays), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtactt-gtccttgctaatgt-accatttttttcttattttat-ttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttat-gcag
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-------CTGAATGCTGGAATAAGATATGTACAAGGGATGAATGAAGTTTTGGCACCCCTCTTCTTTGTATTTCGGAGTGATCCGGATGATAAAAATGCTGTATGGAgtaagagattgttttttttaccaagttcttagtgccctgcattgtacttctgatagccgaagctttcatgtttgctttagt-----cattactatatcttctgtatcg--tgatcttgctattcggaacccttgtag
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G11760.1 (Glycine max), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacct--cttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
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TGCAAAGTTAAACCCGGGTGTAAGATATGTGCAAGGAATGAATGAGATATTGGCTCCTCTATTCTACGTGTTCAAAAATGACCCAGATGAGGAAAATGCAgtgagtatttgataa----actattttaagtttttgttttatgatctatcaagggtttgcattatcaaacacctgattctctgttattgtccttgattgaattc--------------------------------------
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G36520.1 (Glycine max), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
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TGCAAAGTTGAACTCAGGTATAAGATATGTTCAAGGGATGAATGAAGTATTGGCTCCTCTCTTCTATGTGTTCAAAAATGACCCTGACGAGGAAAATGCAgtaagtac--atccttgc----atgctctctcctacccatcgttctctttca-gtttcaaaatgcttgctgagggccatat--gttgatacaatgtt-------tccatctacata------------------------
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G28660.1 (Glycine max), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
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TGCAAAGTTAAACCCAGGCGTACAATATGTGCAAGGAATGAATGAGATATTGGCTCCTCTATTCTATGTGTTAAAAAATGACCCAGATGAGGAAAATGCAgtgagtatatgctttt---aatcttttcattgtttgtcatatgatctat-----cattggtttgcattatcaaacacct-------gattctctgtta-ttctccttgtttg--taat----------------------
upper sequence: AT4G13730.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 5'ss of exon 6
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
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TGCAAAGTTGAATCCGGGTATAAGATATGTGCAAGGGATGAATGAAATTTTGGCGCCTCTATTCTATGTATTCAAAAATGACCCTGATGAGGAAAATGCGgttagtaaatgagatttctg-tgcattcaaaatttttgaacttctgatttgatagtgaagcctacttct---ggttgtctt---atagcatat--tttgtccatctcct-------------------------------Mapped 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|86076731|gb|DR372488.1|DR372488EST: TGTCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCA GCATACGCTGAATCAGATGCATTTTTCT
genomic: TGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtactt ... agttatgcagGCATACGCTGAATCAGATGCATTTTTCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGCAAAGTTGAATCCTGGCATCAGATATGTACAAGGGATGAATGAGATATTGGCACCTATTTTCTACATCTTCAAAAATGACCCGGATAAAGGAAATGCAgtaagtacttgtccttgctaatgtaccatttttttcttattttatttgtacacatattgttctacctcttttagttctttttgggtaacacaccactagttctcctcgtttgcttaacactggcattttaagttatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA