Sequence
atgc intronic sequence ATGC exonic sequencegtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28760.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 6
---gtt-tgttaaact-tcgttaatcaaaactcgcaaaatgctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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atagttatgtctagctactgctagtatcattggtcaataagttcatgtttatctgaccctgaaagactatctaatttataatgaaacaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTCGCTAAGCGAGTAGGAGCAAG-----------------------------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
--------gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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tgtctacctcctgtcatgcatcattgatcgaaagtt-ctctctgcttatc--tgtccttgaaagactatatatctaatttgtaatggagtaattactttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG-----------------------------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
---gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatattttta-tgacttatga----tcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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ccagtaattcagattgtgtttat---gacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG-----------------------------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
---gtttgttaaacttc-gtta---atcaaaactcgcaaaatgctagctgatatatt-tttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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tatatttattctacttctgtcatgtgtcatatcttg-aaagttctgtttttcagcttatccttgagacactatctaatatgttgggaaataattt--ttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG-----------------------------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 4
--gtttgttaaacttcgt--taatcaaaactcgcaaaatgctagctgatatatttttatgacttatga----tcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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atgcctagtaattcagattgtatttatgacctactca---ttagttgattctctctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGTCTTGCTAAGCGTGTGGGAGCAAG-----------------------------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
--gtttgttaaacttc-gtta---atcaaaactcgcaaaat--gctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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atattaattctacttctgtcatgtgttattgcttgaaagttctgtttttcagctgatccttgagacactatctaatatgttaggaaaataattttta---cagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG-----------------------------------
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
-gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatatttttatgactta---tgatcatatatcct-tttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
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tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG-----------------------------------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|86061221|gb|DR356978.1|DR356978EST: ATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAG ACGATAAAAACAAATTGTGATTGGCACACTT
genomic: ATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAGgtttgttaaa ... ctaatggcagACGATAAAAACAAAT-GTGATTGGCACACTT
EST:
gi|152038570|gb|AV831033.2|AV831033EST: ATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAG ACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAG
genomic: ATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAGgtttgttaaa ... ctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAG
EST:
gi|86061222|gb|DR356979.1|DR356979EST: ATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAG ACGATAAAAACAAATGTGATTGGCACAC
genomic: ATTTAGCATGTCCCGCTTCTCCAATTTTCTACAAATACAACCCCGTTAAGgtttgttaaa ... ctaatggcagACGATAAAAACAAATGTGATTGGCACAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
ttctaat putative branch site (score: 2)
tatccttttcatcttt CT-rich tract
atatttttatgactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatatttttatgacttatgatcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG