Sequence
atgc intronic sequence ATGC exonic sequencegtatgaatttatggttgttgtacaagttattttcataggtccggtgtagttatcgtatctgatttcctaaattttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G24740.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 3
-----------------------------------gtatgaatttatggt-tgttgtacaagttattttcataggtccggtgtagt-tatcgtatctga--tttcctaaattttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
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gtcagttgggagagctgcctccgttagaattgaacatcttaacttgagatgtttcttgcatgctgaatttgttgacagagcggagtatattgaaactgaaactttttggatatacatc--agGTACCTTTGGTCAGGTATTGGAATGTTGGGATAGGGAAAGGAAAGAAATGGTGGCCATTAAGATCATCAGAGGCATTAAGAAGTACAGGGATGCTGCAAT
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 2
-------------------------------------------gtatgaatttatggttgttgtacaagttattttcataggt-ccggtgtagttatcgtatctgatttcctaa--attttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
||| ||||| | || |||| | | | | | | | | | | | | | | | | ||| | | | || ||| |||||||| || || ||||||| |||||||| || |||||||||||||| || |||||||||||||||||
gtaaggtgaaaaacattttgggaatcatatgtttaaatggacagta-gaattcactgt-gttggctaggcttgcattgttgatacttatatcatgtttgcagATAAGATCCATACCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG---------------------------
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 2
------------------------------------gtatgaatttatggttgttgtacaagttattttcataggt-ccggtgtagttatcgtatctg--------atttcctaaattttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
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tgaaaaacatttttggaattatatgttcaaatggacattagaattcactgt-gttggctaggcttgcattgttgatacttttttccatatcatgtttgcagATAAGATACATAGCAAAATGGGTGAAGGAACTTTTGGGCAGGTCTTAGAATGCTGGGATAGAGAAAGGAAGGAAATGGTTGCCGTAAAAATTGTCCGTGG---------------------------
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 3
------gtatgaatttatggttgttgtacaagtt--attttcataggtccggtgtagttat-cgtatctgatttcctaaattttcctt--gtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
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gtacccctttggatctattatttcttgatcattctcaattttctacatcataattcatcatgcatccccgatccaatttatttcctttttgtagGAACCTTTGGTCAGGTTTTGGAATGCTGGGACAGAGAGAGGAAGGAAATGGTTGCCGTCAAAATTGTCCGTGGTATTAAGAAGTATCGTGAGGCTGCCATMapped 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|116482136|gb|EG524728.1|EG524728EST: ATAAAATTTATAGCAAAATGGGGGAAG GTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAA
genomic: ATAAAATTTATAGCAAAATGGGGGAAGgtatgaattt ... ttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAA
EST:
gi|124985167|gb|EL057775.1|EL057775EST: ATAAAATTTATAGCAAAATGGGGGAAG GTACTTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATG
genomic: ATAAAATTTATAGCAAAATGGGGGAAGgtatgaattt ... ttccttgtagGTAC-TTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttcataggtccggtgtagttatcgtatctgatttcctaaattttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
tcctaaa putative branch site (score: 2)
ttttccttgt CT-rich tract
atttcctaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaatttatggttgttgtacaagttattttcataggtccggtgtagttatcgtatctgatttcctaaattttccttgtagGTACTTTTGGTCAAGTGCTAGAATGTTGGGATAGGGAGAGGAAGGAAATGGTGGCAGTAAAAATTGTCCGTGGTGTGAAGAAATACCGTGAGGCTGCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT