Sequence
atgc intronic sequence ATGC exonic sequencegtatggcttgaaagtcttttcagtatcttcaatggcatatattattgtttttacactcgttttgctgctatattgaactgccttctcaggctcagagccctctaattcttgtttcttttctttggattttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43700.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g57854.1 (Oryza sativa), 3'ss of exon 1
gtatggcttgaaagtcttttcagtatcttcaatggcatatattattgtttttacactcgttttgctgctatattgaactgccttctcaggctcagagccctctaattcttgtttcttttctttggattttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
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---------------------ggagtgaagattagcagttagtaatg-----acaatccttcttctcagat-ttgagcaaaactgt---actcaa-----tttagct-ttatttttcatcttgatctctatttcagGGGTTATAAAAGGTTCTTTCGGCGGACTGCTCTTGAGACATCGGATTTTCTTAAAGACGATTGCTTAAAGATAAATTGTACTGTGGGTGTTGTGGTATCT
upper sequence: AT3G43700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G44050.1 (Glycine max), 3'ss of exon 1
gtatggcttgaaagtcttttcagtatcttcaatggcatatattattgtttttacactcgttttgctgctatattgaactgccttctcaggctcagagccctctaattcttgtttcttttctttggattttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
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-------------------ccaggctctcc--ttatatggaaaattgatgctaga-tcagtctgaaagtatgctg--ttgtgttgacatgtgtaaaa---------tcttgatctctttttgtgctttc---atagGGGGTACAAGCGGTTTTTCAGACGGTCTTTGCTTGAAACCTCTGAATTCCTCAAGAATGATTGTTTGAAAATCAACTGTACAGTTGGAGTTGTGGTTTCA
upper sequence: AT3G43700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G05000.1 (Glycine max), 3'ss of exon 1
gtatggcttgaaagtcttttcagtatcttcaatggcatatattattgtttttacactcgttttgctgctatattgaactgccttctcaggctcagagccctctaattcttgtttcttttctttggattttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
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-------------------------tcctta----tatggaaaattgttgctaga-tcagtctgaaagtatgctgttcagatgttgtg---tcaacttgtgtaaaatcttgatctctttttgtgctttt---atagGGGCTACAAGCGGTTTTTCAGACGGTCTTTGCTTGAAACCTCTGATTTCCTCAAGAATGATTGTTTGAAAATCAACTGTACAGTTGGAGTTGTGGTTTCA
upper sequence: AT3G43700.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0009g01030.t01 (Vitis vinifera), 3'ss of exon 1
gtatggcttgaaagtcttttcagtatcttcaatggcatatattattgtttttacactcgttttgctgctatattgaactgccttctcaggct-cagagccctcta----attcttgtttcttttctttggattttgaat-agGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
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------------------------------------atatgtttttgggttagaaattggatggttgata------actatttcttcacattgcataatcatttacaagatttttggtttgttcatttattcttttattcagGGGATACAAGCGCTTTTTCAGACGAGCTTTGCTTGAAACATCAGACTTCCTCAAGGATGATTGCTTGAAAATCAATTGTACTGTTGGAGTTGTGGTTTCAMapped 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|19875077|gb|AU235908.1|AU235908EST: CGTTCACTTGATGGTGGTCCTTATACGCTTAAGTACAGAGGAAGTATGTG GGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCT
genomic: CGTTCACTTGATGGTGGTCCTTATACGCTTAAGTACAGAGGAAGTATGTGgtatggcttg ... ttttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttctcaggctcagagccctctaattcttgtttcttttctttggattttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
ctctaat putative branch site (score: 3)
attttgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggcttgaaagtcttttcagtatcttcaatggcatatattattgtttttacactcgttttgctgctatattgaactgccttctcaggctcagagccctctaattcttgtttcttttctttggattttgaatagGGGATACAAGCGTTTCTTCAGACGGTCCTTGCTTGAGACATCTGACTATCTTAAAGACGATTGCTTGAAAATTAATTGTACAGTTGGAGTTGTCGTTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG