Sequence
atgc intronic sequence ATGC exonic sequencegtaaagatccttaaatctgtttaaaaaaacgattcgaaaagagagattcatatataacatagagtgaatgtgatgaaacagATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGAAACATCTTGAAGCAGAAACCAGAACACCAGACTAATACTCAATCCGGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03530.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G20970.1 (Glycine max), 3'ss of exon 5
-------------gtaaagatccttaaatctgtttaaaaaaacgattcgaaaagagagattcatatataacatag-agtgaatgtgatgaaac-----agATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGAAACATCTTGAAGCAGAAACCAGAACACCAGACTAATACTCAATCCGGCT---
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agtgatgatattcttgcgtgaataaaaattcttttgtagaatattttctgtgcaaatgcttttcctttcctatagtgacaaatatggcgccatttcatagATAATGGAAGTTCCTAGTCTTTTGGAAGAAGGATCTACAGCAGTTAAAAGGAATATTCTAAAGCAACAACAACAACCCCAAGC--AT-CCGAATTTGGTGGTT
upper sequence: AT5G03530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G06780.1 (Glycine max), 3'ss of exon 5
----------------gtaaagatccttaaatctgtttaaaaaaacgattcgaaaagagagattcatat---ataacatagagtg-aatgtgatgaaacagATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGAAACATCTTGAAGCAGAAACCAGAACACCAGACTAATACTC-AATCCGGCT
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aagtgatgacattcttgcatgaataaa-agttctgttgtagagtatttgctgtgcactgcttttcctttcctatagtaacaaatatggcgccatttcatagATAATGGAAGTTCCTAGTCTTTTGGAAGAAGGATCTACAGCAGTAAAAAGGAATATTCTAAAGCAACAACAGGAACAACCC-CAAGCATCCGAATTTGGTG
upper sequence: AT5G03530.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g04740.t01 (Vitis vinifera), 3'ss of exon 5
--------gtaaagatccttaa--atctgtttaaaaa--aacgattcgaaa--agagagattcatatataacatagagtgaatgtgatgaa-----acagATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGAAACATCTTGAAGCAGAAACCAGAACACCAGACTAATACTCAATC-CGGCT
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aaaatttggtcatattgataaaggacctgtataaagggcatctattagaaattatatggaattatatattactgattcatgctgttatgtttacttgcagATAATGGAGGTTCCTAGCCTTTTAGAAGAGGGATCGACTGTAGGGAAGAGAAACATCTTGAAACCGAAACCAGAAAACCA-ACCACCACCTACTGGTGGTTMapped 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|124949227|gb|EL024871.1|EL024871EST: CGAAGAGTTGGCTTTGAAG ATAATGGAGGTTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAG
genomic: CGAAGAGTTGGCTTTGAAGgtaaagatcc ... gatgaaacagATAATGGAGG-TACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAG
EST:
gi|19799975|gb|AU231265.1|AU231265EST: CTATAACTCGACAAAACGTGGGACAGTGTTTCGAAGAGTTGGCTTTGAAG ATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGA
genomic: CTAGAACTCGACAAAACGTGGAACAGTGTTTCGAAGAGTTGGCTTTGAAGgtaaagatcc ... gatgaaacagATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacgattcgaaaagagagattcatatataacatagagtgaatgtgatgaaacagATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGAAACATCTTGAAGCAGAAACCAGAACACCAGACTAATACTCAATCCGGCT
atataac putative branch site (score: 3)
attcatatataacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagatccttaaatctgtttaaaaaaacgattcgaaaagagagattcatatataacatagagtgaatgtgatgaaacagATAATGGAGGTACCTAGTCTCTTGGAAGAAGGATCAAGTGCTGTGAAGAGAAACATCTTGAAGCAGAAACCAGAACACCAGACTAATACTCAATCCGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC