Sequence
atgc intronic sequence ATGC exonic sequenceACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtccttatttgtttcttggtttgcttttgatctcttacacttgcggaaaatagcatgagttacagttaggcttttataaccccatttcttcttcagtgtacctaatccaagtgataaaggtacatgtgttttgaatcatttaacaaaaatggtattctctgttttcaatttgttggtacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13340.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13340.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 5'ss of exon 6
ACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtccttatttgtttcttggtttgcttttgatctcttacacttgcggaaaatagcatgagttacagttaggcttttataaccccatttcttcttcagtgtacctaatccaagtgataaaggtacatgtgttttgaatcatttaacaaaaa-tggtattct-ctgttttcaatttg----ttggtacag---------
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GGTGCACTTCCTGGCTTCAAACAATGATTGTGGAGTTCGAGACTTTGACATGGAAAAATTTCAAATTTGCAATAATTTCCGTTTTCCTTGGGCTGTTAATgtaagcctttacttcattcatcaaactgttt---atatctatatcttgttttattta---ttggatactcccaagtcctaatctattcgccacattcaagtcactactgaatgctttgctaaagattcttgcattcc--atgaggaaagaaagcctaatgttttattgatttaatcttgccccttgttttataccatgcag
upper sequence: AT3G13340.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G113726_T01 (Zea mays), 5'ss of exon 7
ACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtccttatttgtttcttggtttgcttttgatctcttacacttgcggaaaatagcatgagttacagttag-gcttttataaccccatttcttcttcagtgtacctaatccaagtgataaaggtacatgtgttttgaatcatttaacaaaaatggtattctctgttttcaatttgttggtacag
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TCTGCACTTCCTTGCGTCAAACAATGATTGTGGACTTAGAGACTTTGACATGGAAAAGTTTCGAATATGCAACCACTTCCATTTTGCTTGGCCTGTGAATgtaag--cctgcagtgcttgttgaatt---ttcaattttctat-----ctaaatctagct---gctgaagtcaatgctcatgt-------tttgtcaaagagcatgtcttaaataag-gacagaaacacat---tactgcatcct---------gtgttggcccctgtttt-aattttctgcag---
upper sequence: AT3G13340.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA04G12500.1 (Glycine max), 5'ss of exon 8
ACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtccttatttgtttcttggtttgcttttgatctcttacacttg-cggaaaatagcatgagttacagttaggcttttataaccccatttcttcttcagtgtacctaatccaagtgataaaggtacatgtgttttgaatcatttaacaaaaatggtattctctgttttcaatttgttggtacag
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AGTTCATTTCACAGCCGCTAATAATGATAGTGGAGTGAGAGACTTTGATATGGAGAAATTTCAGCTTTCTAAGCATTTTTGTTTTCCCTGGCCAGTGAATgtga-gtccctaagactttttttctttatttccatcttctttcccaagactgataaatggatattttagttttattccttcagaaat---tgtgttaccaggtg-----------------------------------------------------------------------------------
upper sequence: AT3G13340.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv19s0015g01750.t01 (Vitis vinifera), 5'ss of exon 7
ACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtccttatttgtttcttggtttgcttttgatctcttacacttgcggaaaatagcatgagttacagttaggcttttataaccccatttcttc-ttcagtgtacctaatccaagtgataaaggtacatgtgttttgaatcatttaacaaaaatggtattctctgttttcaatttgttggtacag
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AGTTCACTTCATTGCCTCAAGTAATGACTGTGGAGTTAGAGACTTTGATATGGAAGATTTTCAACTTTCTAAGCACTTTCATTTTCCTTGGCCAGTGAATgtaag----ttgcatatatcagaattttcatttgtttagatctaatta-gaaacttgctacttttcagatttagacctaaaaattctttgctataagtttagtgg----------------------------------------------------------------------------------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|47831951|gb|CK121635.1|CK121635EST: TGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAAT CACGCATCTTTGAGTCCTGATGGTAAATTACTGGCTATTGTTGGAGACAAC
genomic: TGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtcct ... gttggtacagCACGCATCTTTGAGTCCTGATGGTAAATTACTGGCTATTGTTGGAGACAAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACTTCATTTTACTGCGTCAAATAATGACTGTGGAGTTAGAGACTTTGACATGGAGAGATACCAGCTTGTTAAGCATTTCCGTTTTCCTTGGCCAGTGAATgtaaagtccttatttgtttcttggtttgcttttgatctcttacacttgcggaaaatagcatgagttacagttaggcttttataaccccatttcttcttcagtgtacctaatccaagtgataaaggtacatgtgttttgaatcatttaacaaaaatggtattctctgttttcaatttgttggtacag
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA