Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttactgttagattttgttaacattattagatagagaatatttggtaataacttcattggaaatgtatattgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G27300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------gtgagtttactgttag--attttgt-taacattattagatag---agaatatttggtaataacttcattg--gaaatgtatattgtttcca--gCTGATCTT------GGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA---------
|||| | || || | ||| ||| | || | || | | | || | ||| | | || || || ||| || || ||| | |||||||||||| | |||||||||| |||||||||||||| ||||| |||||||| | | ||| | || |||| | | |||||
gtaaagtttctttactattccatacgttattctttttggaatttatacaagctatgcgctctagttgaacaaaagcaatgaagcataaagttagtggaaaattcaggtcttcttggaagcatttcttcatcaagattcattttctttgcataaatgttctgtttgcagCTGGATGGACTAGAGTCATTGTTGAGAAGCCATTTGGAAAGGACTTGGACTCTGCAGAAGAATTAAGTGCCCAACTTGGGGAGCTATTTGACGAAAACCA
upper sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 5
--gtgagtttac---tgttagattttgtta-----acattattagatagagaata-tttggtaataact-tcattggaaatgtatattg----tttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
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acttaattttacttcttttgaacctctttaggcccagtctatcaatcaaacattgcttttatagtttttattgatgattgtatctattaacattttgtagCTGATCTTGGTGGGTGGACACGTATTGTTGTTGAGAAGCCTTTTGGTAAGGATCTGGAATCTGCAGAGCAACTCAGTACCCAGATTGGACAGTTGTTTGA
upper sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 5
------gtgagtttactgttagattttgt-------taacattatt-agatagagaatatt--tggtaataacttcattggaaatgtatattgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
| ||| || ||| ||||||| | ||||| ||| | |||| | | ||| | | | || | || | | || ||||||||||||||||||||| | |||||||||||||||| ||||| |||||| | |||||||||||| | || ||| || |||||||| ||||||||
ttgtctttactttttcttttacattttgtggttcctttttattatccagaaatctaatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA
upper sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 5
------gtgagtttactgttagattttgttaac----attattagatagag----aatatt--tggtaataacttcattggaaatgtatattgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
| ||| || ||| ||||| | |||||| ||| | || | | ||| | | | | || | || | | || ||||||||||||||||||||| | ||||||| ||||| || ||||| |||||| | |||||||||||| | || ||| || |||||||| ||||||||
ttgtctttacattttcttttacattttatggttcctgtttattatccagaaatctagtactgattgtattgatatgactgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTCGAGAAGCCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA
upper sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
------------gtgagtttactgttagattttgttaacattattagatagagaatatttggtaataacttcattggaaatgtat-------attgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
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taagattcccagttcaagtagatgctgaagcctaccagtat--ttaggttcagaacctgtaaatctagatct-ttatgaatgccttgatgtgatcttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGAMapped 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|125023963|gb|EL096232.1|EL096232EST: TGTATACCCTCCTGTAAGCAAGATGATCAAGGCATGGTGCACTAACAAAT CTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGG
genomic: TGTATACCCTCCTGTAAGCAAGATGATCAAGGCATGGTGCACTAACAAATgtgagtttac ... ttgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattagatagagaatatttggtaataacttcattggaaatgtatattgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
taataac putative branch site (score: 1)
ttgtttcc putative PPT
aatatttggtaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttactgttagattttgttaacattattagatagagaatatttggtaataacttcattggaaatgtatattgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG