Sequence
atgc intronic sequence ATGC exonic sequence...tggaatacttgattgcagatatttataatagagaattcagttttgtcttgggaggcagtacttagctgactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06080.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06080.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g05080.1 (Oryza sativa), 3'ss of exon 1
tggaatacttgattgcagatatttataatagagaattcagtt--ttgtcttgggaggcagtact--tagctgactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
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----atacctgtggactgagatgtaccattatcaataaattcaaatgcccatattagcaatgctggtgtctcactctaatttcgtctccttttctgtttcttagATTTAATGCCAGAAATATGCTAGAGAAACTCAGAAACAGAAGAGTTGTATTTGTTGGGGATTCGATTGCAAGAAACCAATGGGAGTCTCTGCTTTGTATG
upper sequence: AT3G06080.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G025250_T01 (Zea mays), 3'ss of exon 2
tggaatacttgattgcagatatttataatagagaattcagttttgtcttgggaggcagtacttagct--gactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
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-tttataactgaaggacaatctgaaagatccacatttccactctagcataatcactaatctttttctctgacttggtcatattctttctttgatttg-ttagATTTGATGCCAAAAGCATGCTGGAGAAGCTACGAAACAAAAGAGTGGTTTTTGTTGGTGATTCAATTGGAAGGAACCAATGGGAGTCTCTACTTTGTATG
upper sequence: AT3G06080.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G004445_T01 (Zea mays), 3'ss of exon 1
tggaatacttgattgcagatatttataatagagaattcagttttgtcttgggaggcagtacttagct--gactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
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-tttataactgaagaccaatctggaagatccacattaccactctagcataatcgttaatctttttctctgactcggtcgtattattcctttgatttg-ttagATTTGATGCCAAAGGCATGCTGGAGAAGCTACGGAACAAAAGAGTGGTTTTTGTCGGTGATTCAATTGGAAGGAACCAATGGGAGTCTCTACTTTGCATG
upper sequence: AT3G06080.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G30910.1 (Glycine max), 3'ss of exon 1
---tggaatacttgattgcagatatttataatagagaattcagttttgtcttgggaggcagtacttagctgactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
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atcttgagtagcattttgcttgtgcatacaataatatgttaggttct-tttagcttggttgt--tggaatgaaatataatgagtgactgtactcttgcaacagATTTGATGCAAAGAATATGTTGGAAAAGCTACGGGACAAGCGACTAGTGTTTGTTGGTGATTCGATTGGAAGGAACCAATGGGAATCACTGCTTTGTATG
upper sequence: AT3G06080.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0104g00120.t01 (Vitis vinifera), 3'ss of exon 1
tggaatacttgattgcagatatttataatagagaattcagttttgtcttgggaggcagtacttagctgactctattttcctgttttgaaaactgaat-tagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
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ttttttttaaattttttaaagactttaattaggaaaaagaataggaagaaggatgttat-tttgatcttttcttttttccttaattctattttgaatacagATTTGATGCAAACGTCATGTTGGAGAAGCTGAGGAACCGGCGGGTTGTGTTTGTTGGTGATTCCATTGGAAGAAACCAATGGGAATCCCTTCTTTGCATGMapped 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|124972030|gb|EL045751.1|EL045751EST: TTGTTCTATACTCAGTGGCGTTGGCAACCTAGACACTGTAATTTGCCCAG ATTTGATGCAAAACTGAT
genomic: TTGTTCTATACTCAGTGGCGTTGGCAACCTAGACACTGTAATTTGCCCAGgtattgattc ... actgaattagATTTGATGCAAAACTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgggaggcagtacttagctgactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
agctgac putative branch site (score: 3)
ttttgaaaa 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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggaatacttgattgcagatatttataatagagaattcagttttgtcttgggaggcagtacttagctgactctattttcctgttttgaaaactgaattagATTTGATGCAAAACTGATGCTGGAGAAACTCCGGGACAAGCGGCTTGTGTTTGTTGGCGATTCAATAGGAAGAAACCAGTGGGAGTCTCTACTTTGTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA