Sequence
atgc intronic sequence ATGC exonic sequencegtttgtccttttctctcatgagaactcttggtggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 19
----gtttgtcc-ttttctctcatgagaactcttggt-ggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
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gttggtttttaaattttttctaaagaaagtatttaatcagttttttgtgttggata-tatttgactaaaagaattgtaatgtt--agGTTTCACTTGTTAGTAAAGACTCCTCCATGTTGGATGGTCTTGACAATGCCAGTATTGAAATGGAAGAAGCCAAG
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 17
gtttgtcct-----tttctctcatgagaactcttggtg-gttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
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gttggtttttaaaatctttctaaagggagtatttaatctgttttttgtgttggata-tctttgactaatataattttaatgtt--agGTTTCACTTGTTAGTAAAGACTCCTCCATGTTGGATGGGCTTGACAATGCCAGTATTGAAATGGAAGAAGCCAAG
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 21
gtttgt--ccttttctctcatgagaactcttggtggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
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gtttgtggtctttcccctgaaaaaaatatttggtctgtttttttatcgaatatgtttgactgatttggttatcttttttgaagGTTTCCCTTGTTAGCAAGGACTACTCCATGTTGGATGGGCTTGAAAATGCAAGTTCTGAAATGAAAGAAGCCAAG
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 17
gtttgtcct-tttctctcatgagaactcttggtggttggtaaggtcatatggtcactaatttcttttcttt-tttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
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gtttgtggtctttcccccgaaaaaaatatt--cgatctgtttttttattggatgcttgactgatttggttaacttttttgaagGTTTCCCTTGTTAGCAAGGACTACTCCATGTTGGATGGGCTTGAAAATGCAAGTTCTGAAATGAAAGAAGCCAAG
upper sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 19
gtttgtccttttctctcatgagaactcttggtggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
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gtttgtagccttccct-aagatctgttttaacagctgttggtgcca---agttataaactgtttttattgtgttttta-agGTTTCCCTTGTTAGCAAGGACTCATCTATGTTGGATGGACTTGACAATGCCAGTATTGAGATGGAAGAAGCTAAGMapped 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|124756146|gb|EH846276.1|EH846276EST: GGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTG GTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCC
genomic: GGCCTGCTTGACCTAGAAGGACAGCTGACGCCAATCCTGgtttgtcctt ... ttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
cactaat putative branch site (score: 2)
tcactaatttcttttc CT-rich tract
actaatttcttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtccttttctctcatgagaactcttggtggttggtaaggtcatatggtcactaatttcttttcttttttttctctagGTTTCTTTGGTTAGCAAGGACTCTTCCATGTTGGATGGTCTTGATAATGCCAGCATTGAAATGGAAGCGGCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG