Sequence
atgc intronic sequence ATGC exonic sequencegtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11670.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 5
gtgaatcatctactctatttcttcaagccttgttctg---ttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
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---------gtgctgtatctagctcaac-ttgttctggtatcatctggatgcacttcagtt-tcagtatt------gctaatgaatggcttatgc-------agGTTTTACGTCTGTCTGCAGCAACTCAGGATCTTCCTAAGTCTATTATTTGCAACGTCCATGGTGTAAATCCAAAGTTCCTTAAGATTGGAGATAAAATAA
upper sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 5
----------------------------------gtga-atcatctactctatttcttcaagcct-tgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
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gtactcaattaagtagggtctgcaatgttcaagtgtgacagtgtgaagtttctatcatgtagctaacgcataagtattcaaaaattatgtaatttagttgattttccttactga-gctgatggttggtacaacgtagGTTTTGCGACTGTCAGGAGCTACACAAGATCTCCCCAAGTCCATGATCTGCAATGTACATGGTGTCAATCCCAAGTTTCTTGAGGTTGGAGAGAGAATTG
upper sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 3
gtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
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--------------gtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcc------taatg----ttattcatctat---agGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGCAATGTTCATGGTGTTAACCCAAAGTTCCTGAAGATTGGAGAAGAAATAA
upper sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G38720.1 (Glycine max), 3'ss of exon 5
-gtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaa-agGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
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ggtgtttttgttgataaatttgtcatggagttctttcatcataaaagaactaaatgaaacaagacaaaaagggactaaat---tatttatgatttatattcagGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTG
upper sequence: AT3G11670.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 5
------gtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
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gttttcgtgtttttgttgataaatttgtcatggagttcttttatcaa--aaaagaactaaacaaaacaaaaagggactaaattatttatgatttatattca-----gGTTCTTCGTCTCTCAGCTGCTACTCAGGATTTACCAAAGTCTGTAATTTGCAATGTTCATGGTGTGAATCCCAAATTCTTGAAAATTGGAGAAAAGATTGMapped 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|125039221|gb|EL111490.1|EL111490EST: TTTTTGTGAACCATGTAAACAATTGGGTCACACGAGCGTATTGTGACAAG GTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAG
genomic: TTTTTGTGAACCATGTAAACAATTGGGTCACACGAGCGTATTGTGACAAGgtgaatcatc ... ctcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAG
EST:
gi|125044263|gb|EL116532.1|EL116532EST: TTTTGTTGAACCATGTAAACAATTGGGTCACACGAGCGTATTGTGACAAG GTTCTTCGCCTCTCTGCGGCAACACAAG
genomic: TTTTG-TGAACCATGTAAACAATTGGGTCACACGAGCGTATTGTGACAAGgtgaatcatc ... ctcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
ttttctactc CT-rich tract
tttactaataaatagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatcatctactctatttcttcaagccttgttctgttgcttgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaagGTTCTTCGCCTCTCTGCGGCAACACAAGATTTACCAAAGTCTGTTGTATGCAATGTCCATGGTGTCAATCCCAAGTTCCTTATGATTGGGGAGAAAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA