Sequence
atgc intronic sequence ATGC exonic sequencegtacattactctcttcaccattttttattttggttcctggctattagtttcaacaacttagtaattcttgaaggcatgttctcaaaaatgcctatatagacatttcatgtttgtggctgaatttccgaaattacatctttaaatgtatgtttatgatttcgcttcactttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62530.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G10610.1 (Glycine max), 3'ss of exon 6
gtacattactctcttcaccattttttattttggttcctggctattagtttcaacaacttagtaattcttgaaggcatgttctcaaaaatgcctatatagacatttcatgtttgtggctgaatttccgaaattacatctttaaatgtatgtttatgatttcgcttca--ctttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
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------------------------------------------------------------------------------aactaacattattctatatggtttccctaggat-gttacaaagctcatataatt---cctttagtgatttctttgttgttttattttaaacaaaatattggcagGTTCGTTTCCTGGCAAGGTCTTTTGCTGTACCTGGAAATCATCTTGGACAACAAAGTCATGGTTTTCGTTGGCCATATGGTCCG
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G01300.2 (Glycine max), 3'ss of exon 6
gtacattactctcttcaccattttttattttggttcctggctattagtttcaacaacttagtaattcttgaaggcatgttctcaaaaatgcctatatagacatttcatgtttgtggctgaatttccgaaattacatctttaaatgtatgtttatgatttcgcttcactttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
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---------------------------------------------------------------------------acattgtcttatgtgatttccctaggatgttacaaagctcatataattcctttagtgatttcttc-----tctgttcttgcttcaatttaacaaaatctttacagGTTCGTTTCCTGGCAAGGTCTTTTGGTGTCCCTGGAAATCATCTTGGACAACAAAGTCATGGTTTTCGTTGGCCATATGGTCCC
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G01290.1 (Glycine max), 3'ss of exon 5
gtacattactctcttcaccattttttattttggttcctggctattagtttcaacaacttagtaattcttgaaggcatgttctcaaaaatgcctatatagacatttcatgtttgtggctgaatttccgaaattacatctttaaatgtatgtttatgatttcgcttcactttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
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-----------------------------------------------------------------------cattatttatttataa-----tatatggtttccctatgat-gttacaaagctcatataatt---cctttagtgatttcttctttgttgtatttaacaaaatattgacagGTTCGTTTCCTGGCAAGGTCTTTTGGTGTACCTGGAAATCATCTTGGACAACAAAGCCATGGTTTTCGTTGGCCATATGGTCCT
upper sequence: AT5G62530.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 6
gtacattactctcttcaccattttttattttggttcctggctattagtttcaacaacttagtaattcttgaaggcatgttctcaaaaatgcctatatagacatttcatgtttgtg-gctgaatttccgaaattacatctttaaatgtatgtttatgatttcgcttcactttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
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-----------------------------------------------------------------------gggcatttttcagctcatgacc-tatggtctcttga-attagtgtgctagggtt----aactgcatttt---atcttttctcatttctccctttcactgtatct-ggcagGTTCGTTTCCTGGCGAGGTCTTTTGCAGTGCCAGGAAATCATCTTGGGCAGCAAAGTCATGGTTTTCGTTGGCCTTATGGTCCGMapped 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|86069296|gb|DR365053.1|DR365053EST: GAGAAGTCTTTGTCACAAGGAAGTTTTTAGAAAACTTTTGTGGTGATCAG GTGCGGTTCCTAGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAG
genomic: GAGAAGTCTTTGTCACACGGAAGTTTTTAGAAAACTTTTGTGGTGATCAGgtacattact ... cttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAG
EST:
gi|125294873|gb|EL308958.1|EL308958EST: AGAAAACTTTTGTGGTGATCAG GTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAG
genomic: AGAAAACTTTTGTGGTGATCAGgtacattact ... cttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAG
EST:
gi|86069297|gb|DR365054.1|DR365054EST: GAGAAGTCTTTGTCACAAGGAAGTTTTTAGAAAACTTTTGTGGTGATCAG GTGCGGTTCCTAGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAG
genomic: GAGAAGTCTTTGTCACACGGAAGTTTTTAGAAAACTTTTGTGGTGATCAGgtacattact ... cttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaaattacatctttaaatgtatgtttatgatttcgcttcactttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
tttcgcttcactttct CT-rich tract
tttaaatgtatgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattactctcttcaccattttttattttggttcctggctattagtttcaacaacttagtaattcttgaaggcatgttctcaaaaatgcctatatagacatttcatgtttgtggctgaatttccgaaattacatctttaaatgtatgtttatgatttcgcttcactttcttttatcagGTGCGGTTCCTGGCACGGTCTTTTGCAATCCCTGGGAATCATCTTGGGCAGCAAAGTCATGGTTACCGTTGGCCTTATGGTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG