Sequence
atgc intronic sequence ATGC exonic sequenceCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatgtatgctcatattctcgtgtttttgtgaaaatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62460.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g36740.5 (Oryza sativa), 5'ss of exon 7
CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatgtatgctcatatt-ctcgtgtttttgtgaaaatcag----------------
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--------------GGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAGgttggtgactgttcgaaatccttttgttcttttatgtatccgca-atccacaggcaaaaaatattccagattatctatagcttgctattttgcacttttga
upper sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 6
CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatgtatgctcatatt-ctcgtgtttttgtgaaaatcag----------------
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TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAGgttggtgactgttcgaaatccttttgttcttttatgtatccgca-atccacaggcaaaaaatattccagattatctatagcttgctattttgcacttttga
upper sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g36740.7 (Oryza sativa), 5'ss of exon 6
----------CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatgtatgctcata-ttctcgtgtttttgtgaaaatcag----------------
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TCTTTAACAGTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAGgttggtgactgttcgaaatccttttgttcttttatgtatccgca-atccacaggcaaaaaatattccagattatctatagcttgctattttgcacttttga
upper sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G118957_T05 (Zea mays), 5'ss of exon 3
CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatgtatgctcatattctcgtgt-------ttttgtgaaaatcag-------------
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CTATTTCTTTTGAGAGCCGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggctcggtgccaatg-gaaatgtttctct---ttcatgtgtatactgtattgacttttgacggaaaagaattccacgaaactatttatacctagcatg
upper sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 6
CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatg-tatgctcatattctcgtgtttttgtgaaaatcag---------------------
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CTATTTCTTTTGAGAGCGGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAGgttggtggctcggtgctaatggaaat------gtttctttcatgtgtatactgtattgagtctattgactcctgaggaaaaagaattccaggatactattcatacc
upper sequence: AT5G62460.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 7
CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgta----------tataaatctttgga-aaaacaaaacacataaataaacccatgtgtatgtatgctcatattctcgtgtttttgtgaaaatcag--------
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CTTTTCCTGCTTCGAGCTGCTGGTTTCCTTCTCCCTTGCTACATTATGGCCTGGGCTATCAGTATATTGCAGCGTCGAAGACAAAGACAGgttagtgtttggctttgcatttttgtatagaataaaatatgaagagaaa---aaatattctccttcaggacctatggtgggtatgccaaaagaaaaaatgcagMapped 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|47829320|gb|CK119004.1|CK119004EST: ACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG GAAGCTGCTGCTCTAGCTGCTGCAGAAGTAGCGTTTATGTTACATAG
genomic: ACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaat ... tgaaaatcagGAAGCTGCTGCTCTAGCTGCGGCAGAAGTAGCGTTTATGTTACATAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAGgtatataaatctttggaaaaacaaaacacataaataaacccatgtgtatgtatgctcatattctcgtgtttttgtgaaaatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA