Sequence
atgc intronic sequence ATGC exonic sequencegttcatataaaactaatcttatctttgattaaaactaaaaaaatggcttcacttataatctctctggttttgttttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 9
-----------gttcatataaaact----aatcttatctttgattaaaactaaaaaaatggcttcactt---ataatctctctggttttgttttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
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ctgcctagagaatttagcaagagtcacacaactcaatctcttttgtgaagtttttggtttggtccattttgcatgatatggtta-tgctatttcctttcagTGTAAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGAATATTTGGAAAAG
upper sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G07480.1 (Glycine max), 3'ss of exon 9
---------gttcatataaaactaatcttatctttgattaaaactaaaaaaat--ggcttcacttataatctc---tctggtt---ttgttttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
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tactgcctagtgaatgtagtaagagtcacaactcagtctctttcgtgaagtttttggtttggtccattttgcatgatatggttatgttatttcctttcagTGTAAGGGCAATAGTTGCTTTGAACCTTCATAGCTATGGAAGTGGAAGAAATCCATGGGGTAAACCAAAACCAGATTATTTGGAAAAG
upper sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G30040.1 (Glycine max), 3'ss of exon 2
--------------gttcatataaaactaatcttatctttgattaaaactaaaaaaatggcttcacttataatctctctggttttgt--tttggtgt-agCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
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tcaaagttcttatagcttacattagtgtgataaaatttgttcttatggtctcattagaggtttgtctcattttaaataaggttatgtcatttgttttcagTGTAAGAGCAATAGTTGCTCTAAATCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTGACACCTGAGTATTTAGAGAAG
upper sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G22370.1 (Glycine max), 3'ss of exon 2
------gttcatataaaactaatcttatctttgattaaaactaaaaaaatggcttcacttataatctctct-----------ggttttgt--tttggtgt-agCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
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tttgaagctcttatagtat--acattag-tgtgataacaattgttcttatggtttcgttttgggtttctctcttttaaataaggttatgtcctttgctttcagTGTAAGAGCAATAGTTGCTCTAAACCTTCATAGTTATGGAAGTGGAAGAAATCCATGGGGTAATTTAACACCTGAGTATTTAGAGAAG
upper sequence: AT4G30340.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 9
--------------gttcatataaaactaatcttatctttgattaaa-actaaaaaaatggcttcacttataatctctctggttttgttttggtgt--agCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
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caaaatagcaacctttttttattttttatttctttttcttgatttattattagtatcatttattcatttcatttcacttaatgtttctttcaacttcaagTGTGAGGGCAATAGTTGCTTTGAATCTTCATAGCTATGGAAGTGGAAGACATCCATGGGGTAATCTGAAGCCAGACTATTTGGAAAAGMapped 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|164170159|gb|ES026632.1|ES026632EST: TTAAAAAGGCAAATTGTTCCGAGTGGGAAGAGATCCATGTTCCTAAGAG CGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACA
genomic: TTAAAAAGGCAAATTGTTCCGAGTGGGAAGAGATCCATGTTCCTAAGAGgttcatataa ... tttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaactaaaaaaatggcttcacttataatctctctggttttgttttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
aactaaa putative branch site (score: 2)
ttttgtttt putative PPT
actaaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcatataaaactaatcttatctttgattaaaactaaaaaaatggcttcacttataatctctctggttttgttttggtgtagCGTAAGATCTATTGTGGTGTTGAATCTTTATAACTATGGAAGTGGAAGACATCCATGGGGTAATCTCAGACCAAAATATTTAGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA