Sequence
atgc intronic sequence ATGC exonic sequence...tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22410.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 2
tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcgg--tgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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---------------------gtgcttttctatcgtcgcccatgttaactctagtaatg-agctcagagctatgcagttttttgattggtgtgctttggcagGTTTACAACAGAGCAGGTTCGTAATCTTGATAGGAACAAGCAGTGGTCTAGAGCTCTTGATGGCTCCAATTATCTACCTGGAATG
upper sequence: AT4G22410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 2
tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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-----gtgcttcttcat----tgcttctaacattacatttcaatagcacttgatggctttggcaacacaggctgctaattagtgtactgttc--tggcagGTTCACTAAGGAGCAGGTTCTAAATCTTGACAAAAATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG
upper sequence: AT4G22410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 3
--tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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attctctgt-tctctttatgttgttgttaccttgaattctttaaatgattaactactaatatgcattatctaagttcattcatatg-gttatctatctgcagATTCACTGCAAAAGAAGTTGAACAACTTGACAAAAATAAGCAGTGGTCTAGGGCTCTTGATGGTTCTAGTTACCTTCCCGGAATG
upper sequence: AT4G22410.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 3
--tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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attctctgt-tctctttatgctgttgttaccttgaattctttaactgttaaactactaatatacatgatctaagttcattcatgtg-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|164090486|gb|ES196161.1|ES196161EST: CTTCTTTGGATGACATTCGCCATGTTTTAAACCCAAG GTTTAGTAGAGCACAAGTAGACGAGCTTGACAAGAATAGGCAGTGGTCTAG
genomic: CTTCTTTGGATGACATTCGCCATGTTTTAAACCCAAGgtatattaga ... ccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttatattttttcatattactcttctttcatgttttctcaatttttctttgatttttcagttcctttttatgaaggcttcggtgctatccatttacagGTTTAGTAGAGCACAAGTAAACGAGCTTGACAAGAATAGGCAGTGGTCTAGGGCTCTTGATGGCTCCGACTATCTTCCAGGAATG
- - - - - - - - - - -ctcttct