Sequence
atgc intronic sequence ATGC exonic sequence...gaaaattccatacaatttttttgcctggtctccaatgttcttataatgttgtatctgattggttttgacatattgctgtgttatgtacggcttatctcagGTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTCCGGAGTGATGTCACCAGATTCTTGACGACTATACTTATTGGAACAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 1
gaaaattccatacaatttttttgcctggtctccaatgttcttataatgttgtatctgattggttttgacatattgctgtgttatgtacggcttatc------tcagGTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTCCGGAGTGATGTCACCAGATTCTTGACGACTATACTTATTGGAACAAC
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----gtccccaccttgtttatcatccattaaaccctgttggttgatggtagtccttttcatgtctaaaca-attgatgc-ttagatttggttttctgttccactagGTTCGTGAGTTGGCTGAAAAGGAACCTGAAAATGGTGTTTTCAGAATGCTCCGAAGTGATGTTACTCGCTTCCTGACAACCATACTCATTGGCACAAC
upper sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 1
---gaaaattccatacaatttttttgcctggtctccaatgttcttataatgttgtatctgattggttttgacatattgctgtgttatgtacggcttatctcagGTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTCCGGAGTGATGTCACCAGATTCTTGACGACTATACTTATTGGAACAAC
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cttatgtatctagattacttttcttgtttcatctccctagtaaatgttctaacctattgga--gattttgtgattgtgttggttgatat-tgttttatatcagGTGCGTGAGTTAGCTGAAAAGGAGTCTGAGAATGGTGTCTTCAAAATGCTCCGCAGTGATGTTACTCGTTTCTTAACGACTATACTTATAGGCACAACMapped 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|125053989|gb|EL124881.1|EL124881EST: TCTATGGCAGAGACGTCCATTACCACTCTGTGGCCGTGGAAG GTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTC
genomic: TCTATGGCAGAGACGTCCATTACCACTCTGTGGCCGTGGAAGgtaaaatcag ... cttatctcagGTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttgtatctgattggttttgacatattgctgtgttatgtacggcttatctcagGTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTCCGGAGTGATGTCACCAGATTCTTGACGACTATACTTATTGGAACAAC
ttttgac putative branch site (score: 3)
cttatctc putative PPT
acatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaattccatacaatttttttgcctggtctccaatgttcttataatgttgtatctgattggttttgacatattgctgtgttatgtacggcttatctcagGTGCGTGAGTTGGCTGAGAAAGAACCAGAGAATGGTGTATTCAGAATGCTCCGGAGTGATGTCACCAGATTCTTGACGACTATACTTATTGGAACAAC
- - - - catacaa
- - - - - - - - - - - - - - tctccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttttg