Sequence
atgc intronic sequence ATGC exonic sequencegtatgttacctactgaagctagactcttatagtataagtttccacagagtatacaaatgtttttattactgtttctcattcttttctggtccaaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38240.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G426275_T04 (Zea mays), 3'ss of exon 11
gtatgttacctactgaagctagactcttatagtataag-tttccacaga-gtatacaaatgtttttattactgtttctcattcttttctggtc-caaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
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------------------gtatgttatgttattatatgctttctacatacaaatatgaggaacttgatatataaatttccttttattctaatcattgttgtacggaagGACGATTATGGCTGTTTCTTCTTGGAATGACAATGGGCAGAAGCAGTTTGTTAACGACCCAA
upper sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G00200.1 (Glycine max), 3'ss of exon 11
gtatgttacctactgaagctagactcttatagtataagtttccacagagtatacaaatgtttttattactgtttctcattcttttctggtc-caaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
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gtatgtgttctagaagcgcagaatgctgaatttat---tttcttttgattcactgcactagttttttaagactccggaatctctgttgttaatatttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
upper sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA06G00230.1 (Glycine max), 3'ss of exon 11
gtatgttacctactgaagctagactcttatagtataagtttccacagagtatacaaatgtttttattactgtttctcattcttttctggtc-caaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
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gtatgttttctagaattgcagaatgctgaatttat---tttcttttgattcgctacactagttttttaagactttggaatctctgttgataatttttctattctagATCCATTATGGCTGTTTCCTCATGGAATGACAATGGACAAAAGCAGTTTGTACATGATCCAT
upper sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv00s0972g00010.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttacctactgaagctaga-ctcttatagtataagtttc---cacagagtatacaaat---------gtttttattactgtttctcattcttttctggtccaaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT--------------
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gtgtgtcttttggatgaactaaagctcatataagttaaatttcatttttagaagttattaattaacttcagagttctgatgttttttctgcacttaccttggtataaaaccatgatagGTCCATTATGGCTGTTTCTTCATGGAATGACAATGGGCAAAAGCAGTTTGTGCATGATCCTTGTAAGCTCTTCTGA
upper sequence: AT4G38240.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv00s0585g00030.t01 (Vitis vinifera), 3'ss of exon 11
gtatgttacctactgaagctaga-ctcttatagtataagtttc---cacagagtatacaaat---------gtttttattactgtttctcattcttttctggtccaaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
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gtgtgtcttctggatgaactaaagctcatataagttaaatttcatttttagaagttattaattaacttcagagttctgatgttttttctgcacttacctcggtataaaaccatgatagGTCCATTATGGCTGTTTCTTCATGGAATGACAATGGGCAAAAGCAGTTTGTGCATGATCCTTMapped 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|125300365|gb|EL314450.1|EL314450EST: TGGATAGGGATAA AACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGT
genomic: TGGATAGGGATAAgtatgttacc ... catgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacaaatgtttttattactgtttctcattcttttctggtccaaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
aatgtttttattact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttacctactgaagctagactcttatagtataagtttccacagagtatacaaatgtttttattactgtttctcattcttttctggtccaaacatgtgttagAACCATTATGGCTGCTTCATCATGGAATGATAATGGACAGAAGCAGTTTGTGCATGATCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC