Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatgccttgaatgaggttcttagagctttatgtaaaaggtgcgcatttctcagaattatactcgtgagttcttaactgttcctccaccaattggttgcagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCTTTTAAGCTTCTTCAGATTGATGAAGAATTTAATATTTTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01230.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 2
gtatgtatgccttgaatgaggttcttagagctttatgtaaaaggtgcgcatttctcagaattatactcgtgagttcttaactgttcctccaccaattggttg-cagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCTTTTAAGCTTCTTCAGATTGATGAAGAATTTAATATTTTTGAAG
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---------------------gtatgattgatttgtattacaga---gtgttcttc----ttctttttgtagggttgcattcatgcttagctaaattggttttcagGATATCTATTACCGGAAAGCAAAAGAAGAAGGTTGGCGTGCTCGAAGTGCCTTTAAACTCCTTCAGATAGACGAGGAATTCAACCTTTTTGAAG
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G07970.4 (Glycine max), 3'ss of exon 2
gtatgtatgccttgaatgaggttcttagagctttatgtaaaaggtgcgcatttctcagaattatactcgtgagttcttaactgttcctccaccaattggttg-cagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCTTTTAAGCTTCTTCAGATTGATGAAGAATTTAATATTTTTGAAG
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----gtatggtt--gatttgtctttcagagtgttcttcat--------ctttttggggggttgcattcatg----cttagcta----------aattggttttcagGATATCTATTACCGGAAAGCAAAAGAAGAAGGTTGGCGAGCTCGAAGTGCGTTTAAACTCCTTCAGATAGACGAGGAATTCAACCTTTTTGATG
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtatgccttgaatgaggttcttagagctttatgtaaaaggtgcgcatttctcagaattatactcgtgagttcttaactgttcctccaccaattggttgcagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCTTTTAAGCTTCTTCAGATTGATGAAGAATTTAATATTTTTGAAG
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----gtgggtttaatttctcattct-aatttcttctgttcaatttccg-gtgtgt-----tttcatttttcagtttttag-taaaggttgattagt---ttgcagGATATCTACTATCGTAAAGCAAAGGAAGAAGGTTGGCGTGCTCGAAGTGCCTTCAAACTCCTTCAGATTGATGAGGAATTCAACATATTTGAAGMapped 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|86044361|gb|DR340116.1|DR340116EST: CTCCGTATTCTACTTTAGAGGCCATGGGAAAAGCTTCTCGAGACAAAAGG GATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCT
genomic: CTCCGTATTCTACTTTAGAGGCCATGGGAAAAGCTTCTCGAGACAAAAGGgtatgtatgc ... ttggttgcagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCT
EST:
gi|86044363|gb|DR340118.1|DR340118EST: CTCCGTATTCTACTTTAGAGGCCATGGGAAAAGCTTCTCGAGACAAAAGG GATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCT
genomic: CTCCGTATTCTACTTTAGAGGCCATGGGAAAAGCTTCTCGAGACAAAAGGgtatgtatgc ... ttggttgcagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctcagaattatactcgtgagttcttaactgttcctccaccaattggttgcagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCTTTTAAGCTTCTTCAGATTGATGAAGAATTTAATATTTTTGAAG
tcttaac putative branch site (score: 2)
agaattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgccttgaatgaggttcttagagctttatgtaaaaggtgcgcatttctcagaattatactcgtgagttcttaactgttcctccaccaattggttgcagGATATCTATTATCGTAAAGCTAAAGAAGAAGGATGGCGTGCAAGAAGTGCTTTTAAGCTTCTTCAGATTGATGAAGAATTTAATATTTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG