Sequence
atgc intronic sequence ATGC exonic sequence...cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22285.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 2
cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcgg--tgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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------------------gtgcttttctatcgtcgcccat---gttaactctagtaatg-agctcagagctatgcagttttttgattggtgtgctttggcagGTTTACAACAGAGCAGGTTCGTAATCTTGATAGGAACAAGCAGTGGTCTAGAGCTCTTGATGGCTCCAATTATCTACCTGGAATG
upper sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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-----gtgcttcttcat-tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaa-----ttagtgtactgttctggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
upper sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 3
-cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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attctctgttctctttatgttgttgttaccttgaattctttaaatgattaactactaatatgcattatctaagttcattcatatg-gttatctatctgcagATTCACTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCCGGAATG
upper sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 3
-cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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attctctgttctctttatgctgttgttaccttgaattctttaactgttaaactactaatatacatgatctaagttcattcatgtg-gttctctatctgcagATTCGCTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCTGGAATGMapped 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|86059785|gb|DR355542.1|DR355542EST: GAGATCAATGACCCTTCTTTGGATGACATTCGCCATGTTTTAAACCCAAG GTTTAGTAGAGCACAAGTAGACGAGCTTGACAAGAATAGGCAGTGGTCTAG
genomic: GAGATCAATGACCCTTCTTTGGATGACATTCGCCATGTTTTAAACCCAAGgtatattaga ... ccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
ctttgat putative branch site (score: 5)
tccattt putative PPT
tttttatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgatagcttgaacatattactcttctttcatgtcttgtcaaattttctttgattttacagttcctttttatgaaggcttcggtgttatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
- - - - - -gaacata
- - - - - - - - - - -ctcttct