Sequence
atgc intronic sequence ATGC exonic sequencegtaaattctctcgcatttccttcttccctttcactctaatttcgtttgattccgtcttttaaatctgagccacttgaattaggctttgtgattgaacctctgaggctaagaaatttgaaaatctggttgatgtgtagGTGAAGTTAGATCCATCAAGGCCTTTGAGCAAGAATAAGCATTGGATTGTTGCAGAAATCATCAAAAAAGCTCGAATTTATTCTCCTAAAGCTGCTGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49400.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0070g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtaaattctctcgcatttccttcttccctttcactctaatttcgtttgattccgtcttttaaatc-tgagccacttgaattaggctttgtgattgaacctctgaggctaaga-aatttgaaaatctg-gttgatgtgt-agGTGAAGTTAGATCCATCAAGGCCTTTGAGCAAGAATAAGCATTGGATTGTTGCAGAAATCATCAAAAAAGCTCGAATTTAT---TCTCCTAAAGCTGCTGCTG
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-------------------------------------------------gtcagttgttaaagcaatgggttccttcctttctccacttccgttttttcataatggataaaataacttgtgaaacaacactgtcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCAGAAATTCTGAAGAAAGCACGAATCTATGTGCCACCTGAACCTATTA---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|164154330|gb|ES010597.1|ES010597EST: CGACAAAGACGCCTGCAACATTGGCGATCGA GTGAAGTTAGATCCATCAAGGCCTTTGAGCAAGAATAAGCATTGGATTGTT
genomic: CGACAAAGACGCCTGCAACATCGGCGATCGAgtaaattctc ... tgatgtgtagGTGAAGTTAGATCCATCAAGGCCTTTGAGCAAGAATAAGCATTGGATTGTT
EST:
gi|164234711|gb|ES022354.1|ES022354EST: CCAAATTCATGGCTCACGACGACAAAGACGCCTGCAACATCGGCGATCGA GTGAAGTTAGATCCATCAAG
genomic: CCAAATTCATGGCTCACGACGACAAAGACGCCTGCAACATCGGCGATCGAgtaaattctc ... tgatgtgtagGTGAAGTTAGATCCATCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttgtgattgaacctctgaggctaagaaatttgaaaatctggttgatgtgtagGTGAAGTTAGATCCATCAAGGCCTTTGAGCAAGAATAAGCATTGGATTGTTGCAGAAATCATCAAAAAAGCTCGAATTTATTCTCCTAAAGCTGCTGCTG
ggttgat putative branch site (score: 5)
taagaaatttgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattctctcgcatttccttcttccctttcactctaatttcgtttgattccgtcttttaaatctgagccacttgaattaggctttgtgattgaacctctgaggctaagaaatttgaaaatctggttgatgtgtagGTGAAGTTAGATCCATCAAGGCCTTTGAGCAAGAATAAGCATTGGATTGTTGCAGAAATCATCAAAAAAGCTCGAATTTATTCTCCTAAAGCTGCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT