Sequence
atgc intronic sequence ATGC exonic sequenceACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09810.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 7
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag
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ATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaa-atttgttatt--gtttgttctatca--atttgacatccaggtaatacaacg---ccaactaactattttgcactctcccag
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G404855_T01 (Zea mays), 5'ss of exon 6
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttc-------ttcgtctcacagattattg-tctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag-------
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ATCCTGGTCTTTTTGATGTATTAGTGATGCCAAACCTCTATGGTGACATCATTAGCGATCTATGTGCTGGTTTGATTGGGGGCTTGGGCCTAACACCCAGgtaa-atttgctttgattaatctaattttgttgggtattgatatggcaaaaggacaggcctggagccaaaggtcctgagtttgatgcagcctctctgcaat
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G120857_T02 (Zea mays), 5'ss of exon 6
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag
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ATCCTGGTCTTTTTGACGTATTAGTGATGCCAAATCTCTATGGTGACATTATTAGTGATCTATGTGCTGGTTTGATCGGGGGCTTGGGCCTAACACCCAGgtaa-acttg---ctttgtttaatctaatttccttgggtattgataca--gcaaa-agctcacatttgt-ttgtttattttcccag
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 5
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag
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ATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCTTAACACCAAGgtatc-ttcatttattc-tatcatctttaatttatatgattcatatagatcctcacatctttcgg-cttcctacacag--------
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S78_143V6.1 (Physcomitrella patens), 5'ss of exon 5
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggca-atcatcttatgctctta----ttatgttttgttccag
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ATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTTTGACACCAAGgtgaccttcatccc-------cataaatctttacatgcgaaataagtgtttagtatcatcccaaaccctgaactcttgatcttcgttgcag
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S83_44V6.1 (Physcomitrella patens), 5'ss of exon 5
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtcta-gta-tgaaaatgaggcaatcatcttatgctcttattatg-----------ttttgttccag-
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ACCCCGCATTATTTGATGTATTGGTAATGCCTAATCTTTACGGTGATATCATCAGCGATTTGTGCGCTGGTCTAATTGGCGGTCTAGGGCTGACGCCTAGgtaggattgacttctcaaaacttgataacattcttgaagtgctgagcatgtattggtgattgcaaattagttctaggacgggagaggcctttaaatcaga
upper sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 5
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcg---tctcacagattattgtctag--tatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag---------
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ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgaggattggttttcaccacaacaaaagtagtagctaggatttaagcMapped 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|125169277|gb|EL193402.1|EL193402EST: ATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAG TATGAATATTGGGGAGGATGG
genomic: ATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttg ... tttgttccagTATGAATATTGGGGAGGATGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA