Sequence
atgc intronic sequence ATGC exonic sequence...gatgtctgagtacttgaaactccttatggaaaagtcttaccttgaaaaacttctttcttgatgatgatgttttctgataaaagtgtctctctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTGAGTAAGACAGCTCCAATCCAAGCCATTTCACTCCTCATCTTTGGTCCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G21070.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G21070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G00210.2 (Glycine max), 3'ss of exon 3
gatgtctgagtacttgaaactccttatggaaaagtcttaccttgaaaaacttctttcttgatgatgatgttttctgataaaagtgtctct--ctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTGAGTAAGACAGCTCCAATCCAAGCCATTTCACTCCTCATCTTTGGTCCAT
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-acttactactact-aaagtcaattgtggtatatgctattattttgtgatgtttgggggatttcttcttttttataactgtttttttttcaacttgtaacagTCAATAGGTTCTCTTCAAAAGAAATATTCAATTGGATCTTTTGAATTGCTGAGTAAAACTGCTCCCATCCAAGCGCTTTTTCTTCTTATTCTTGGTCCAT
upper sequence: AT1G21070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G45700.1 (Glycine max), 3'ss of exon 3
gatgtctgagtacttgaaactccttatggaaaagtcttaccttgaaaaacttctttcttgatgatgatgttttctgataaaagtgtctct----ctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTGAGTAAGACAGCTCCAATCCAAGCCATTTCACTCCTCATCTTTGGTCCAT
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--tttct-actact-aaagtcaattgtggtatatgctattattttgtgatgtttgtgggatttattcttttttataactgatttttattttcaacttgtaacagTCAATAGGTTCTCTTCAAAAGAAATATTCAATTGGATCTTTTGAATTGCTGAGTAAAACTGCTCCCATTCAAGCGCTTTTTCTTCTTATTCTTGGTCCAT
upper sequence: AT1G21070.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0122g00090.t01 (Vitis vinifera), 3'ss of exon 3
--gatgtctgagtacttgaaactccttatggaaaagtcttaccttgaaaaacttctttcttgatgatgatgttttctgataaaagtgtctctctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTGAGTAAGACAGCTCCAATCCAAGCCATTTCACTCCTCATCTTTGGTCCAT
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acatcttatgcttaatggattttgctggttcgtgatgtttgtgtggaaagagt--tttattcatgtcctctgacaatgagtggaaaattttctgtgatacagTCAATAGGTTCTTTGCAAAAGAAGTACTCAATTGGATCTTTCGAATTGCTGAGTAAAACTGCTCCGATTCAGTCCATCTCCCTCCTTGTGCTTGGTCCATMapped 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|19877654|gb|AU238485.1|AU238485EST: GTTTCATTTGTGCTTGCACTGCCGTTTTCTCCACTTCTCTCCAGCAGATC TCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTG
genomic: GTTTCATTTGTGCTTGCACTGCCGTTTTCTCCACTTCTCTCCAGCAGATCgtaagctttt ... ctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaacttctttcttgatgatgatgttttctgataaaagtgtctctctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTGAGTAAGACAGCTCCAATCCAAGCCATTTCACTCCTCATCTTTGGTCCAT
ttctgat putative branch site (score: 3)
tgtctctct putative PPT
tgataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgtctgagtacttgaaactccttatggaaaagtcttaccttgaaaaacttctttcttgatgatgatgttttctgataaaagtgtctctctggaaacagTCAATAGGTTCACTGCAGAAGAAATACTCGATCGGATCATTCGAGTTGCTGAGTAAGACAGCTCCAATCCAAGCCATTTCACTCCTCATCTTTGGTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - -ttgaaac
- - - - - - - - - - - - - -ggaaaag
- - - - - - - - - - - - - - - - - - - - - tgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaaa