Sequence
atgc intronic sequence ATGC exonic sequence...ttattactctgtatttcactatgcaaaccctgttaaaagaaaaaaagattaatggttttggcaaaattctcacaatgtgtaacaattccaaactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G40470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G092517_T01 (Zea mays), 3'ss of exon 2
ttattactctgtatttcactatgcaaaccctgttaaaagaaaaaaagattaatggttttggcaaaattctcacaatgtgtaacaattccaaactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
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--gtaaagcctcaacttgaagaaaaaatcgtgcttttctagtctatagttaaaagatttcagtgtagacttgtaa-acgtgtcgattgtca------cagGAGGTGGTGGAGGGGGAGAGGGCGGACACAGCGAGCAGCCTGGTGTACGAAGCGAACCTCCGGTTGCGGGATCCGGTGTACGGATGCATGGGCGCCATCT
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G39830.1 (Glycine max), 3'ss of exon 1
-ttattactctgtatttcactatgca-------aaccctg-ttaaaagaaaaaaagattaatggttttg---gcaaaattctcacaatgtgtaacaattccaaactaat----cagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
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gtaaatacacacacacacactgtacacataaataacactggctagctagttatctaattaatcatatcatatacatgtgtattccacttattatagatttcaatcatatgttgtagGAAGTACCAGAGTGTCAAAGAGCTGATGCAGCAAATAGTCTAGTATATGAGGCTAATGTGAGGCTAAGAGATCCTGTGTATGGATGCATGGGTGCAATTT
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G15050.1 (Glycine max), 3'ss of exon 1
-----------------------------ttattactctgtatttcactatgcaaaccctgttaaaagaaaaaaagattaatggttttggcaaaattc--tcacaatgtgtaacaattccaaactaat----cagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
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gtaaatatacacacacacggtacacataaataacactagctagctagttatttaattaaccatatcatataacatgtattccacttattatagattttaatcatatcatataatttcttcgacaatgtgttgtagGAAGTACCAGAGTGTCAAAGAGCTGATGCTGCAAATAGTCTAGTTTATGAGGCTAATGTGAGGCTAAGAGATCCTGTGTATGGATGCATGGGTGCAATTT
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0067g02380.t01 (Vitis vinifera), 3'ss of exon 2
ttattactctgtatttcactatgcaaaccctgttaaaagaaaaaaagattaatggttt-tggcaaaattctcacaatgtgtaacaattccaaactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
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----------gtagaacccta-attctgtctaccagtagtatttcatgttcttgattgattgataacttctcaaa---tcttacactgttaaatt---cagGAAGTCCCGGAAAGCCAAAGAGCCGACGCCGCCAATAGTCTGGTTTATGAGGCCAATGTGCGGCTAAGAGATCCGGTCTATGGTTGCATGGGTGCAATTTMapped 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|86082783|gb|DR378542.1|DR378542EST: CCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGYTAATG GAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAA
genomic: CCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagcca ... aactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattaatggttttggcaaaattctcacaatgtgtaacaattccaaactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
aaaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattactctgtatttcactatgcaaaccctgttaaaagaaaaaaagattaatggttttggcaaaattctcacaatgtgtaacaattccaaactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAAGCAAACGTGAGGCTAAGAGATCCGGTGTACGGATGCATGGGAGCCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - -caaaccc
- - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaacaa