Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttctcattcagattctttctcttgttcttaagaaatgtttggtttctaataatataatgttttggatcatatattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCCAAGCTGGTCCAGTAGGCAATGTACAGTCAGAGCTTCTCTTCCAAAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29810.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------gtaagtttct---------cattcagattctttctcttgttcttaagaaatgtttggtttctaataatataatgttttggatcatatattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCCAAGCTGGTCCAGTAGGCAATGTACAGTCAGAGCTTCTCTTCCAAAAGAA
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gtaagcgtgatcctaacttgtttcgatttctggagttaaaagctttcttaaatactgtgaatattttcttaattcttcatcataaaacatcaaaacttttacttcttattttgataaac-tatagaaggtaattac-tgat-ttttaagttgcttttaacagATGATACTGCAATGCTATGGGGAGTTAAGTTCTATAATGATTTTCTCAACCAAGCTGGCCCTAATGGCAATGTTCAATCAGAGCTACTCTTCCGAAAGGA
upper sequence: AT3G29810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G22410.1 (Glycine max), 3'ss of exon 5
gtaagtttc-tcattcagattctttctctt----gttctt----aagaaatgtttggtttctaataatataatgttttggatcata-tattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCCAAGCTGGTCCAGTAGGCAATGTACAGTCAGAGCTTCTCTTCCAAAAGAA
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gtaagttctatctttcatagccacaatcctagatgatcttgtgaagaaaataccacaattcttatgttat--tgatttgcaatatggttttacagATGATACAAGTATGCTGTGGGGAGTCAAGTTCTACAATGATTTTCTTTCTTCAGCTGGATCTCTTGGTAATGTTCAGTCAGAAATCTTACTTAGAAAAGA
upper sequence: AT3G29810.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G32130.1 (Glycine max), 3'ss of exon 5
gtaagtttc-tcattcagattctttctctt----gttctt----aagaaatgtttggtttctaataatataatgttttggatcatatattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCCAAGCTGGTCCAGTAGGCAATGTACAGTCAGAGCTTCTCTTCCAAAAGAA
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gtaagttctatctttcatagtcacattcctagatgatcttgtgaagaaaataccccaattcttatgttattgatttgcgaaatg-gttttacagATGATACAAGTATGCTGTGGGGAGTCAAGTTCTACAATGATTTTCTTTCTTCAGCTGGATCTCTTGGTAATGTTCAGTCAGAAATCTTACTTAGAAAAGAMapped 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|86082822|gb|DR378581.1|DR378581EST: TCAGCTTTTCAGTTTCAACTACAAACCGCTTAATCCTTACTTGAACATAA ATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCC
genomic: TAAGCTTTTCAGTTTCAACTACAAACCGCTTAATCCTTACTTGAACATAAgtaagtttct ... tatattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttaagaaatgtttggtttctaataatataatgttttggatcatatattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCCAAGCTGGTCCAGTAGGCAATGTACAGTCAGAGCTTCTCTTCCAAAAGAA
ttctaat putative branch site (score: 2)
taataatataatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttctcattcagattctttctcttgttcttaagaaatgtttggtttctaataatataatgttttggatcatatattgaagATGACACGGCCATGCTATGGGGAATCAAGTTCTACAATGATTTTTTAAGCCAAGCTGGTCCAGTAGGCAATGTACAGTCAGAGCTTCTCTTCCAAAAGAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA