Sequence
atgc intronic sequence ATGC exonic sequencegtttgctattgaccaagttactcatctctttgtacgacattgggtttctattttttcccacatgttcaaaggagctgtatcatgttttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13320.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 8
---------gtttgctattgaccaagttactcatctctttgtacgacattgggtttctattttttcccacatgttcaaaggagctgtatcatgttttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA
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gtcagtaccattttttgtt-actggatttctttgccttttccttgccgttttggatctttgaagtcttgtttaccagctattagtatgctggaatttttttaagtcactgtcctgtaagcctggcctccctcttcaaaaaagttctgttgattggtgaattttgtttt----gatctttcagGTTATTGGCATTGACTTTTTATCCCAAACACTGCTACCAGCCATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 8
-----------gtttgctattgaccaagttactcatctctttgta-cgacattgggtttctattttt-tcccacatgttcaaaggagctgt-atcatgtt----ttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA
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gtcagtaccattttttttgttattagatttatttgccttttcctttctgttttagatttttaatgtaatcttttataagctagctagccattagtatgctagatttttttaagttgatgtc--cttgaaagccttgcctttctcttcaaaattatc-tgatgatt-gctgatttttgttttgatctttcagGTTATTGGAATTGACTTGCTATCTCAATCACTGCTACCAGCAATTGTAGAACTTGCAGAGGATAGGCACTGGAGAGTCCGGCTTGCAATAATTGAGTACA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 8
gtttgctattgaccaagttactcatctctttgtacgacattgggtttctattttttcccacatgttcaaaggagctgtatcatgttttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA
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--------------------------------------------------------------agaataggctttttttttaaacttgtgttcaag---atgttt-cctggcatcattcacttcattcaatgatgtact-------tgtaagttctctcctgtatttttttcagGTTATTGGAATTGACTTGTTGTCGCAATCACTTCTGCCAGCCATTGTAGAGCTCTCTGAAGATAGGCACTGGAGAGTTCGGCTTGCCATAATTGAGTACAMapped 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|164028967|gb|ES050171.1|ES050171EST: TTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAG GTTATTGGGATTGATCTACTAT
genomic: TTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAGgtttgctatt ... aaattgccagGTTATTGGGATTGATCTACTAT
EST:
gi|116425639|gb|EG468231.1|EG468231EST: TTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAG GTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAA
genomic: TTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAGgtttgctatt ... aaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAA
EST:
gi|86073296|gb|DR369053.1|DR369053EST: TTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAG GTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAA
genomic: TTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGAACCAGgtttgctatt ... aaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA
ttttttttccttaa CT-rich tract
atttttcataatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgctattgaccaagttactcatctctttgtacgacattgggtttctattttttcccacatgttcaaaggagctgtatcatgttttggtcaagtcaatgactacttgacagcaaattctttgtccatccatttttcataatgattcgattttttttccttaaaattgccagGTTATTGGGATTGATCTACTATCACAATCGTTACTGCCAGCCATTGTAGAACTTGCTGAAGACAGGCACTGGAGAGTACGTCTGGCTATAATCGAGTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA