Sequence
atgc intronic sequence ATGC exonic sequencegtgagctaatttaacataagacccatgatgttcgttctattgatttggctccattcccctgcacatttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 4
gtgagctaatttaacataagacccatgatgttcgttctattgatttggctccattcccctgcacatttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
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gtaagcc--tgtggctttttcattgtaaaaatttctctatgtgactgtgaaaggcaaataacctgttcgtgtcaactctt---agGCCAAATGTCGAGAAACAGGAGAAATTGTTGCCATTAAAAAGGTTCTTCAAGATAAACGTTACAAGAACAGGGAATTGCAAATTATGCATATGCTGGATC
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 4
gtgagctaatttaacataagacccatgatgttcgttctattgatttg------gct--ccattcccctgcacatttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
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gtgagtttgcttttcatatctcttctaaacaccatgctgttgatgtatgacatactgatgataccttcttcgttttatcaatgcttttattagGCAAAATGTAGAGAAACAGGAGAAATTGTGGCCATCAAGAAAGTTCTCCAGGACAAACGATACAAGAATAGAGAGTTACAAATTATGCAAATGCTGGATC
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G00400.2 (Glycine max), 3'ss of exon 3
gtgagctaatttaacataagacccatgatgttcgttctatt---gatttggctccattcccctgcacattt-atgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
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gtgagttttcttt-tgtaaaccccatcttgtttatcgtatttcagacatgctgatgataccttcttcattttattaatgcttttatcagGCCAAATGTAGAGAAACGGGAGAAATTGTGGCCATCAAGAAAGTTCTCCAGGACAAGCGCTACAAGAATAGAGAGTTACAAATTATGCAAATGCTGGATC
upper sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
gtgagctaatttaacataagacccatgatg--ttcgttctattgatttggctccattcccctgcac-------atttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
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gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtgagatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACCMapped 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|124929686|gb|EL007209.1|EL007209EST: CATATCAGAACATGTTGTTGGTACTGGTTCCTTTGGCATAGGTTTTCCAA GCTAAATGTAGGGAAACTGGGGAGGTTGT
genomic: CATATCAGAACATGTTGTTGGTACTGGTTCCTTTGGCAT-GGTTTTCCAAgtgagctaat ... cttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgttctattgatttggctccattcccctgcacatttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
tattgat putative branch site (score: 3)
tttatgtttcctttt putative PPT
atttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctaatttaacataagacccatgatgttcgttctattgatttggctccattcccctgcacatttatgtttccttttggtagGCTAAATGTAGGGAAACTGGGGAGGTTGTTGCCATCAAGAAGGTTCTACAAGACAAACGCTACAAGAACAGGGAGCTACAAATAATGCAGATGCTAGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG