Sequence
atgc intronic sequence ATGC exonic sequencegtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G74030.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g20820.1 (Oryza sativa), 3'ss of exon 3
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtca-atcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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--------------------------------gtctgcagtcatcttgttttatttcccaccttttcaatgtggaccaccttttttttttttgtaacttataatactgtgaacccatcctact---gcagATTAAAATTGGAATGGATGTTGCAGCATCAGAGTTTCTTACAAAGGATGGAAGCTATGACTTAAACTTTAAGAATCAGCCTAATGATGGAGCTCATGTTC
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G034848_T01 (Zea mays), 3'ss of exon 3
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctg--tgtttccctaaacaacttctggcagcttcggtgtcaatcttacacc-actcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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------------------------------------------gtgtgatatcatctaactagtttcattggccacttgtt-tgattgttctcttgattttattttgaattttaaaacaaatc-ctaatgcagATCAAAATTGGAATGGATGTTGCGGCATCAGAGTTCCTTACAAAGGATGGGAACTATGATCTAAACTTTAAGAATCAGCCTAATGATGGAGTCCATGTTC
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G25390.1 (Glycine max), 3'ss of exon 4
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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-------------------------------------gtgaagctttg-attatttctgttgc-----atactttgaatattcacttgtgctgatctggaa--------ataaaaaaaaatggt-gcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G22780.1 (Glycine max), 3'ss of exon 4
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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---------------------------------gtgggtgaagctttg-attatttctgttgc-----ataatttgaaaattcacttgtgctgatctggaa--------ataaaaaacaatggt-gcagATTAAAATAGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAGCCAAATGATGGAGCTCATGTTC
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G23080.1 (Glycine max), 3'ss of exon 3
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttt--tgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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-------------------------------------------------gtgggtgatgctttgattatttctgttacataatttgaatattca-cttgtgctgatctggaaataaaaaacaatggcgcagATTAAAATAGGCATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCAAGAAACAACCAAATGATGGAGCTCATGTTC
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G24920.1 (Glycine max), 3'ss of exon 2
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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---------------------------------gtgggtgaagttttg-attatttctgttgc-----ataatttgaatattcacttgtgctgatctggaa--------ataaaaaacaatggt-gcagATTAAAATTGGTATGGATGTTGCAGCTTCAGAGTTTTACACTAAGGATGGGAAGTATGATTTGAACTTCATGAAACAGCCAAATGATGGAGCTCATGTTC
upper sequence: AT1G74030.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g04540.t01 (Vitis vinifera), 3'ss of exon 3
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
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--------------------------------------gtaggcgggttgttgcttttcttttcttttgcagttt-----gattttccttgcagcctttaaggactc------caaataaatgatgcagATCAAAATAGGAATGGATGTTGCAGCTTCAGAGTTCTTCACTAAAGATGGGAAATATGATTTGAATTTTAAGAAACAACCAAATGATGGAGCTCACGTTCMapped 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|164022559|gb|ES032002.1|ES032002EST: GTTCTGCTCATAGATGCAATTGAAAAGGCCGGTTACACTGGAAAG ATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATG
genomic: GTTCTGCTCATAGATGCAATTGAAAAGGCCGGTTACACTGGAAAGgtaatcaagt ... atttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
cactcac putative branch site (score: 2)
tttttgc putative PPT
actcacataatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcaagttctctttctttttaatgctaatacttgctaaagttgcatgtcatctgtgtttccctaaacaacttctggcagcttcggtgtcaatcttacaccactcacataatatataatttttgcagATCAAAATAGGAATGGATGTTGCTGCATCAGAATTTTTCATGAAAGATGGTAGATACGATTTGAACTTCAAGAAACAGCCAAACGATGGAGCTCACGTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA