Sequence
atgc intronic sequence ATGC exonic sequenceGATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtattaacggaatcaaagtctttttttgcgtgttgtttgctagttcattataggagatgctgaattggttttcatgacttgattag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14680.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 5'ss of exon 2
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgta----ttaacggaatcaaa------gtc---tttttttgcgtgttgtttgctagttcattataggagatgctga-attggttttcatgacttgattag---------------------------------------------
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GATGGGTTACAAAAATCCTGTTCTTCTGCTTCATCCATTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtag
upper sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G051270_T02 (Zea mays), 5'ss of exon 3
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtattaa-----cggaatcaaagtctttttttgcgtgt----tgtttgctagttcattataggagatg-ctgaattggttttcatgactt--gattag--
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GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatttagatgctataattatactctcccctttcatctcaaattctcaataattggcttcatgttttctccgcagtagcagctatgtctctgaactaaac
upper sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G149952_T01 (Zea mays), 5'ss of exon 2
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtatt-aacggaatcaaagtctttttttgcgtgttgtttgctagttcattataggagatgc---tgaattggttttcatgacttgattag-------------
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GATGGGTTATAAAAACCCTGTTCTTCTGCTCCATCCACTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAACATGAGAAGgtatccagctggat--agttctactcttccctttcatct-cagaataattgggttccatgtccttgaactaaacatcttgttttgatgggatctgctatgtca
upper sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G28980.2 (Glycine max), 5'ss of exon 2
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgt-----attaacggaatcaaagtctttttttgcgtgttgttt---gctagttcattataggag----atgctgaattggttttcatgacttgattag---
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GATGGGTTATAAGAATCCTGTCCTCTTGCTTCATCCACTGGGAGGCTACACCAAAGCTGATGATGTCCCACTTGATTGGCGAATGAAACAACATGAGAAGgtgtgtgatgtactaaaccaaatacttttatagtctcatggttgaagctatgtcactttctgtgcctttttctgttttgattgtaatc-tttgctttgcta
upper sequence: AT4G14680.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 5'ss of exon 2
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgt--attaacggaatcaaagtcttttt-------ttgcgtgttgtttgctagttcattataggagatgctgaattggttttcatgacttgattag--------------------------------
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GATGGGCTACAAGAACCCTGTCCTCTTACTTCATCCATTAGGAGGCTATACAAAGGCAGATGATGTTCCGCTTGGTTGGAGAATGAAGCAACATGAGAAGgttcatgaactgatcctatgatgtattgctcaatttgaaaatcagttatccctctgccagaagggtccattatgtaattgccttaccttcagttctaattctgattaatattgaaaatgttcctcagMapped 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|47830057|gb|CK119741.1|CK119741EST: CAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAG GTGCTAGAGGATGGTGTTCTTGATCCAGAGACTACTGTGGTTTCCATATTC
genomic: CAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtattaacgg ... acttgattagGTGCTAGAGGATGGTGTTCTTGATCCAGAGACTACTGTGGTTTCCATATTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATGGGTTATAAAAACCCTATCCTTTTGCTTCATCCATTGGGAGGGTTTACAAAAGCTGATGATGTTCCTCTAAGCTGGCGAATGAAACAGCACGAGAAGgtattaacggaatcaaagtctttttttgcgtgttgtttgctagttcattataggagatgctgaattggttttcatgacttgattag
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG