Sequence
atgc intronic sequence ATGC exonic sequencegtataaatgaacgtaatcacataaaagattgagatttagcaagtctttagtaccttctaatgtgtgattttattttccttagTGTGAAGCAGTTGGCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTTATGTCGCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79500.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 4
----------------gtataaatg--aacgtaat--cacataaaagattgagatttagcaagtctttagtaccttctaatgtgtgattttattttcc-ttagTGTGAAGCAGTTGGCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTTATGTCGCCAG-
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aattggttcttccagtgtatacttgtcattggaatgtggtattgatagttcagattc--taactcatggtctgcctttggcacgt--ttatattttttgccagtGTGAAGCAGTTGGCAGAGTTGCAGATATCATTCAGATTCCAGCATTCTTGTGTCGCCAAG
upper sequence: AT1G79500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 5
-------------------gtataaatgaacgta--atcacataaaagattgagatttagcaagtctttagtaccttctaatgtgtgattttattttcc-ttagTGTGAAGCAGTTGGCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTTATGTCGCCAG
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aaattgattcttccagtgtatacttaggaatggagtatggtattgatatttcagattc--taactcatgatctgcctttgacgcat--ttatattttttgccagTGTGAAGCAGTTGGCAGAGTAGCAGATATCATTCAGATTCCAGCATTCTTGTGTCGCCAA
upper sequence: AT1G79500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gtataaatgaacgtaatcacataaaagattgagatttagcaagtctttagtaccttctaatgtgtgattttattttccttagTGTGAAGCAGTTGGCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTTATGTCGCCAG
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tgttcagtagtgaaaattttcggctaatatagaatatgttta-gtggagaattggtactcacaatgtcttt--taactgtt--tttagcccttgatttttcccagTGTGAACCAGTTGGCAGAGTTGCAGACATCATTCAGATTCCAGCTTTCCTCTGTCGTCAGMapped 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|152035142|gb|BP846049.2|BP846049EST: AGGTAGCATATGATCTACCAATAGTAACTGATGTTCATGAATCAAGCCAG TGTGAAGCAGT
genomic: AGGTAGCATATGATCTACCAATAGTAACTGATGTTCATGAATCAAGCCAGgtataaatga ... ttttccttagTGTGAAGCAGT
EST:
gi|163998526|gb|ES047080.1|ES047080EST: TGAATCAAGCCAG TGTGAAGCAGTTGGTCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTT
genomic: TGAATCAAGCCAGgtataaatga ... ttttccttagTGTGAAGCAGTTGG-CAAGGTTGCAGATATAATTCAGATTCCAGCATTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgagatttagcaagtctttagtaccttctaatgtgtgattttattttccttagTGTGAAGCAGTTGGCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTTATGTCGCCAG
ttctaat putative branch site (score: 2)
ttttattttcctt putative PPT
attttattttcctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaatgaacgtaatcacataaaagattgagatttagcaagtctttagtaccttctaatgtgtgattttattttccttagTGTGAAGCAGTTGGCAAGGTTGCAGATATAATTCAGATTCCAGCATTCTTATGTCGCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT