Sequence
atgc intronic sequence ATGC exonic sequence...cttcttgtttactcttatattattgttttataaacagttttgtagattttgatataagaaatgaatctgctaaatgatggtaaaatataattctattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34500.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 1
cttcttgtttactcttatattattgttttataaa--cagttttgtagattt---tgatataagaaatgaatctgctaaatgatggtaaaatataattc-tattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT
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-----ataacaatgctgcatctttagtatgttaattcagtgtgaaacctttctgtcatattcccatcttatttgaaaattcatg-tgcattattatacgtaactagGGGTCAAGCTGAGAAGGAGTTTAAAGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAAAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 1
---cttcttgtttactcttatattattgttttataaa-cagttttgt-agattttgatataagaaatgaatctgctaaatgatggtaaaatataattctattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT
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atgctgctgcatctttagtatgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgta---cataatt--aactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT
upper sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0063g02510.t01 (Vitis vinifera), 3'ss of exon 1
cttcttgtttactcttatattattgttttataaacagttttgtagattttgatataagaaatgaatctgc-taaatgatggtaaaatataattctatt-cagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT
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--gagcaatttttggaatgcaattcatatttatttatattaactttcttttacctaaaaaattcctggatgtaaattcatctgatatttgttttgtttgtagAGGGCAGGCACAGAGGGAGTTCAAGGTGGAAGTTGAAGCCATTGGAAAAGTAAGACATAAGAACTTGGTAGGCCTAGTTGGGTATTGTGCAGAAGGTCCCMapped 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|125004787|gb|EL077056.1|EL077056EST: GGTTCTGTCGCCGCCGTCAAGAATCTCCTTAACAACAA GGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGT
genomic: GGTTCTGTCGCCGCCGTCAAGAATCTCCTTAACAACAAgtaatgtctt ... ttctattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgatataagaaatgaatctgctaaatgatggtaaaatataattctattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT
tgctaaa putative branch site (score: 2)
ttctattc putative PPT
taaatgatggtaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcttgtttactcttatattattgttttataaacagttttgtagattttgatataagaaatgaatctgctaaatgatggtaaaatataattctattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - -ataaaca
- - - - - - - - - - - - - - - - - - gttttgt
- - - - - - - - - - - - - - - - - - - - - - gattttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - taagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatat