Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcaactcgtagcgcatgcaattctatatatttattttatgtgattgagtaagactgtaaatttgtcatttcatagtacaaaaaaataatcgaagctttctactttttgaaagcattgaatagGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGAGCAACTAAAGTAACGGACCTAGAAAAACTTGAAAATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39630.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G52810.1 (Glycine max), 3'ss of exon 6
gtgagttcaactcgtagcgcatgcaattctatatatttattttatgtgattgagtaagactgtaaatttgtcatttcatagt-acaaaaaaataatcgaagctttctacttt--ttgaaagcattgaat---agGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGAGCAACTAAAGTAACGGACCTAGAAAAACTTGAAAATCAG-
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-tgagtctaatttaaactgta-gta--tcttaaaatctattc-atgtcga-aagtcaaa-tgcctctgtatcacactatgcttgttgataattaattaaggctttcttctttccttgaaagcattgtattacaggGAATGATGCATTCACGTGGTGAACTACTTCTTATGCTTGATGCTGATGGAGCAACTAAAGTCACTGACCTAGAAAAGCTTGAAAATCAGG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G10150.1 (Glycine max), 3'ss of exon 6
gtgagttcaactcgtagcgca-tgcaattctatatatttattttatgtgattgagtaagactgtaaatttgtcatttcatagt-acaaaaaaataatcgaagctttctacttt--ttgaaagcattgaat---agGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGAGCAACTAAAGTAACGGACCTAGAAAAACTTGAAAATCAG
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gtgagtcttatttaaactatagtttcttaaaatctattcatgttgaatg-tcaaatggctctgta------tcacactatgcttgttgataattaattaaggcttttttctttccttgaaagcattgtattacagGGAATGATGCATTCACGTGGTGAACTACTTCTTATGCTTGATGCTGATGGAGCAACTAAGGTCACTGACCTAGAAAAGCTTGAAAATCAG
upper sequence: AT2G39630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv13s0019g01230.t01 (Vitis vinifera), 3'ss of exon 6
gtgagt---tcaactcgtagcgcatgcaattctatatatttattttatgtgattgagtaagactgtaaatttgtcatttcatagtacaaaaaaataatcgaagctttctactttt-tgaaagcattg---aatagGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGAGCAACTAAAGTAACGGACCTAGAAAAACTTGAAAATCAG
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gtgagtctgttagcctatttattcttcagtcagctacaaatattttcc-tattctatgatgggtctatttttctctattttgtgtgacgacaatttattgaagcactttacctctgtgaaagcattggaaaacagGGGATGCTTCATTCACGTGGTGAACTACTTCTGATGCTGGATGCTGATGGGGCAACCAAGGTTACTGACCTAGAAAAACTTGAAAATCAGMapped 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|125253455|gb|EL267540.1|EL267540EST: ATACCCCTTGGGAAGAATCAAGGCAAAGGAGAAGCTATAAGAAAA GGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGA
genomic: ATACCCCTTGGGAAGAATCAAGGCAAAGGAGAAGCTATAAGAAAAgtgagttcaa ... cattgaatagGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatagtacaaaaaaataatcgaagctttctactttttgaaagcattgaatagGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGAGCAACTAAAGTAACGGACCTAGAAAAACTTGAAAATCAG
tagtacaaaaaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcaactcgtagcgcatgcaattctatatatttattttatgtgattgagtaagactgtaaatttgtcatttcatagtacaaaaaaataatcgaagctttctactttttgaaagcattgaatagGGAATGTTGCATTCGCGGGGTCAGCTACTTCTCATGTTGGATGCTGATGGAGCAACTAAAGTAACGGACCTAGAAAAACTTGAAAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA