Sequence
atgc intronic sequence ATGC exonic sequencegtaaataccagccaattttctaaccattttacttgctcgactgttaagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11270.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 4
gtaaataccagccaattttctaaccattttacttgctcgactgttaagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
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-------------------------------------------------------gtacataacttgctgagttgctggagttttt-cacttgcttgctcagtg--tttaatttg--ttttttcctttacagAATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
gtaaataccagccaattttctaaccattttacttgctcgactgttaagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
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------------------------------gtatgtctgggggatgagatgc---tggagtgtttcacttgcttgct-cagtgttta-----atatttttg-ttgcc-----------------cttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
----------------------------gtaaataccagccaatt---ttctaaccattttacttgctcgactg-ttaagttgcatctgacat----acttgatttactttctgcatta-gttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
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ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttat-tttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 4
-----------------------------gtaaataccagccaatt-ttctaaccattttacttgctcgactg-ttaagttgcatctgacat----acttgatttactttctgcatta-gttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
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gtacaaattaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatat-tttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 4
gtaaataccagccaattttctaac-------cattttact--tgctcgactgttaagttgcatctgacata-cttgattt------actttctgcattagttat---atccatatatctaattgccttgatccga-acttctctct--ctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
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gtaagaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATTGCTGCTCATGAAGTTGAGGAAATTG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 4
-----gtaaataccagccaattttctaaccattttact--tgctcgactgttaagttgcatc-tgacatacttga----------tttactttctgcattagttatatccatatatctaattgccttgatccga-acttctctct--ctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
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gtacaactaagaatatcataatgttttttcatttagctggtgcatgattgatcagttacatcataccaagcttgaatatggccagtttactgttta-agaagctccactgatattacttagtggtttactctaatgcttgcttatggttacagAATGCCACTCAGAAAAGCCAGAAAGTTTTTGTCCACATACCTTCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGMapped 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|124776964|gb|EH866907.1|EH866907EST: ACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAAGAG AATGCTACCCAGAAAAGCCAACGGGTTTTTGT
genomic: ACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAA-GAGgtaaatacca ... ctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGT
EST:
gi|19875108|gb|AU235939.1|AU235939EST: CTTTGGAATTCCCCACAAAAGCATACTATGCGGTTGAGGAGGNGAAAGAG AATGCTNCCCANAAA-GCCAACAGGTTTTTG
genomic: CTT-GGAAT-CCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAGgtaaatacca ... ctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
cttctctctctgc CT-rich tract
ttatatccatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataccagccaattttctaaccattttacttgctcgactgttaagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA