Sequence
atgc intronic sequence ATGC exonic sequencegttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04140.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 11
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
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---------------------------------------------------------------------------------ctaaccctt--ttggtggacaattctgtagttctgatcatttaattttggactgatgtg---atatgaaatct-gttctgcatgatgatattttta-----ttcgctgcagTTTTCACCTACATCAGAGCACATACTACTGGCATATGGTCGTCGTCATAACTCACTTCTGAGGGGCATTTTCATGGATGGCAAGACCACAATCCCTGTGT
upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 12
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatacttta-taattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
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--------------------------------------------------------------------------------------gactggcttttgcatttttgacctaaacttgagaaatattgata--tgaaattcaaca-----actttcttcatcagttaatttggtgagcacttgtttttctgcagTTCTCACCCACTTCAGAGCACATACTATTGGCATATGGTCGTCGTCATAACTCTATGCTTAGGAGCATTGTGATGGATGGGGAAACTGGAATTCCTGTAT
upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 11
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagag-ttgttcacttgta-tttttgtgatgaaat---actttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
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------------------------------------------------------------------------------------------------caaaaaagcatttaggacctgagtc-tgatgacagatggatcttacatttttgcagttttcatcattgaattggatcctgtttgtctctcttttgatgcagTTCTCACCTACATCCGAACACATACTTTTGGCATATGGTCGTCGTCATAGCTCGCTCCTTAGGAGCATAGTTGTGGAAGGCGAAAATGGGGTTCCCGTAT
upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 11
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttc-cttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT----
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-----------------------------------------------------------------------------------tttgttgcaaaaagccaaaaaccacttaggaccttagtc-tgat--caaagataatt-----cttacatttctgcagttctcatcgttgaacctctc--ttttcatgcagTTCTCACCTACATCCGAACACATACTTTTGGCATATGGTCGTCGTCATAGCTCGCTGCTTAGGAGCAT----AGTCGTGGAGGGAGAAAATGGGATTCCTGTAT
upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 10
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
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------------------------------------------------------------------------------------tcaacttttaggggctaagttttattaaattgg---tcaaata-taatttgaaatggcctttt---cttagaggactgaat-ttgtgcaactgctgtttgatatgcagTTCTCACCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGCCATGGTTCTCTTCTTAAAAGTATTGTCATTGATGGAGAAACAACATTACCTATAT
upper sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 10
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
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--------------------------------------------------------------------------------taactcatgttgcaacttttaggggcc---aagttttattaaattggtcaaatataatt-tgaaatggccttctcttagaggattgaattgctgtttgatat--------agTTCTCGCCTACATCTGAGCACATACTACTTGCGTATGGTCGGCGTCATGGTTCTCTTCTTAAAAGTATTGTTATCGATGGAGAAACAACATTGCCTATATMapped 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|125108137|gb|EL161182.1|EL161182EST: TGTCCCGGGCAATTAGGGCTGCACATTGCTTAACCTCTATCCAG TTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATG
genomic: TGTCCCGGGCAATTAGGGCTGCACATTGCTTAACCTCTATCCAGgttagccaca ... ttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATG
EST:
gi|125303257|gb|EL317342.1|EL317342EST: CAATTAGGGCTGCACATTGCTTAACCTCTATCCAG TTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGT
genomic: CAATTAGGGCTGCACATTGCTTAACCTCTATCCAGgttagccaca ... ttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
tttccgt CT-rich tract
ttgtatttttgtgatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccacaatttggttggattaaataaatttgttagacataagtctctgttgcaacttttttctagacataacattgttcaagtacttcataactgcaaagttccttgagatttcacccctaatagtaaatagagttgttcacttgtatttttgtgatgaaatactttataattaaaaatttccgtgcagTTCTCACCAACCTCCGAGCACATTCTGCTTGCATATGGTCGTCGTCATGGTTCTCTTTTGAAGAGCATTGTGAGTGATGGAGAAACAACATCACATTTTT
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