Sequence
atgc intronic sequence ATGC exonic sequencegtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53520.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 4
gttta-gctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacaga-actattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
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gtttgtgttaatttatgattctaatcctttggaaaagagaaataagtatatttgaagtttagcattacttactattaaagatgcctcatttccagACATTGCGGAAACAGCCAATGACAGTTTATGGTGATGGAAAGCAGACTAGAAGTTTTCAATATGTTTCAGATTTG----
upper sequence: AT3G53520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 4
----gtttagctcct-tcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
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gttcgtttaacacgtaccgctattttattaacttttggttacacatttgcgctgtcaatatgaaatt--ctgagtttatacatgat-tatcattgtagGCATTGCGTAGACAGCCTATGACAGTTTATGGTGATGGAAAACAAACTAGAAGTTTTCAGTATGTTTCTGATCTG----
upper sequence: AT3G53520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 5
gtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
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gttcgtttgctacat-attatggactctatttttcttagttgtgatcctattatg-catgtaagcagccatatgat------tgtccttgaagGCACTACGAAGACAACCAATGACGGTTTATGGTGATGGAAAACAAACTCGAAGTTTCCAATATGTTTCTGATCTG----
upper sequence: AT3G53520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G347717_T02 (Zea mays), 3'ss of exon 4
gtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaact----attgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
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gtttgtctcagtttgtgattctgatgca------ttggagaagaggattatcatagaacttcagcactgcttaaagttggcattgcttcatttctagGCTTTGCGGAAACAACCAATGACAGTTTATGGCGATGGAAAACAGACTAGAAGTTTTCAGTATGTTTCAGATTTG----
upper sequence: AT3G53520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 4
gtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaact----attgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
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gtttgtctcagtttgtgattctgatgca------ttggagaagaggattatcatagaacttcagcactgcttaaagttggcattgcttcatttctagGCTTTGCGGAAACAACCAATGACAGTTTATGGCGATGGAAAACAGACTAGAAGTTTTCA--------------------
upper sequence: AT3G53520.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtttagctccttcatcaacat---aaagacaaccgctttcgtataaagccttttgaaaacactctgacag------aactattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
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gtttgatctcctgacttattttccttacagttctgccaaacacaatgaaccgaatcttagacatttttataa-gttctaaagtttttttaactgttatagct-atgttt-tgcagGCCATCCGCAGGCAACCTTTGACTGTGTATGGTGATGGAAAACAAACACGAAGCTTCCAATATGTCTCTGACTTG----Mapped 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|125192778|gb|EL207732.1|EL207732EST: CAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCTAG ACCATTCGCAAACACCCAATGA
genomic: CAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCC-AGgtttagctcc ... atctatgcagACCATTCGCAAACACCCAATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
ctctgac putative branch site (score: 3)
ttatatctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcagACCATTCGCAAACACCCAATGACTGTTTATGGTGATGGAAAACAGACTCGTAGCTTTCAATATGTTTCTGACTTGGTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA