Sequence
atgc intronic sequence ATGC exonic sequence...tccgtaggcatcatagaagggtccttgaattgtacacacgatcttattcaaggttaacttgaacagtttttctgattgatttcttcacttgacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01320.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g03144.1 (Oryza sativa), 3'ss of exon 6
tccgtaggcatcatagaagggtccttgaattgtacacacgatcttattcaaggttaacttgaacagtttttctgattgatttcttcacttgacttcat-------agGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
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-ccattaata--atctgagcgcagttg---cttagatggggtttagctaaagatttactgccac-gctgttgtgtctgatattggaataggaccttctgtgttttagGCTTTCCGTGATGGACCAACAAACAAAGTGAGAGCAAGAATGTCCGTTGCTTCAGCAATCATATTTGGATCTGTGTTCTGGCGAATGGGGAAAACTCAGA
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G119345_T02 (Zea mays), 3'ss of exon 1
------tccgtagg-catcatagaagggtccttgaattgtacacacgatcttattcaaggttaacttgaacagtttttctgattgatttcttcacttgacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
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gaaataactataaaacatttgaggacaaatgttaagatgtaggttgactatctctcgtcatccatt-----gctttttgtaatgtgtaggatcttttgtgttca--gGCTTTTCGTGATGGACCAACAAACAAAGTGAGATCACGAATGTCTGTTGCTTCAGCAGTTATATTTGGATCTGTGTTTTGGCGAATGGGAAAATCTCAAA
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G41110.1 (Glycine max), 3'ss of exon 6
tccgtaggcatcatag-aagggtccttgaattgtacacacgatcttattcaaggttaacttgaacagtttttctgattgatttct--tcacttgacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
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tagttttggaagataataaaggatcatgtatttcttatac---ccagtataaggagaaaacttatttctcgttcattggattcatgattgtctggctgactagGCTTCCCGTGATGCACCAACAAACAAAGTTCGGGCAAGGATGTCAATTGCATCGGCAATTATCTTTGGGTCAGTATTTTGGAGAATGGGAAATTCTCAGA
upper sequence: AT2G01320.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0011g04670.t01 (Vitis vinifera), 3'ss of exon 6
tccgtaggcatcatagaagggtccttgaattgtacacacgatcttattcaag----gttaacttgaacagttt-ttctgattgatttcttcacttgacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
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---ggaatgattatgcttttgtaattta-tgctttagaagttgttgtctgaatgttattaacttcaacttcttgtcctgtttaaacttgtcgattg-ctaactagGCTTCTCGTGATGGACCAACAAATAAAGTTCGGTCAAGGATGTCAATTGCATCAGCTATAATATTTGGGTCGGTTTTCTGGAGAATGGGACGATCTCAGAMapped 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|86072831|gb|DR368588.1|DR368588EST: ATGGTTGGTGGAGGCAGTTTTTCTTGCTGCTTAAACGTGCATGGATGCAG GCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCA
genomic: ATGGTTGGTGGAGGCAGTTTTTCTTGCTGCTTAAACGTGCATGGATGCAGgtattctcct ... gacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcaaggttaacttgaacagtttttctgattgatttcttcacttgacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
attgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccgtaggcatcatagaagggtccttgaattgtacacacgatcttattcaaggttaacttgaacagtttttctgattgatttcttcacttgacttcatagGCTTCTCGGGATGGGCCAACAAACAAAGTCCGTGCAAGAATGTCTGTTGCATCTGCTGTGATATTTGGGTCTGTTTTCTGGAGAATGGGGAAGTCTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA