Sequence
atgc intronic sequence ATGC exonic sequenceCTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgattttattactctggttccacttgtaaattcaccttctgatgttaaatacagtacttcattgtgtatccagtcttttccatc...
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42500.3 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g59060.2 (Oryza sativa), 5'ss of exon 5
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgattttattactctggttccacttgtaaattcaccttctgat-gttaaatacagtacttcat-tgtgtatccagtcttttccatc-----------------------------------------------------------------------
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CTTTTGGTGGCTTTAAAGGTTCGTTATCCTCAGCGAATTACTATTCTCAGAGGAAACCACGAAAGTCGACAGgtatgtactttttttaaaatgcagattcttgatgtttgcttactg--tcattatatgaaagttaaagcttttgttgcatctcttcattctttgttatcctttctgtgtacaactgtacatgctcacaagtcacaactgatgaactgaatgatgctttttgaatcattttgcag
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G062394_T01 (Zea mays), 5'ss of exon 5
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgattttattactctggttccact----tgtaaattcaccttctgatgttaaatacagtacttca--ttgtgtatccagtcttttccatc
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CTTTTGGTGTCTTTAAAAGTTCGATATCCTCAGAGGATCACCATTCTCAGAGGAAACCATGAAAGCCGACAGgtacacaatttcttgtttgacaaattgttcatgttttcttgctgcattactccattctctgttatcagttgtacaaactaaatttttttactgaattttttgcag-
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G108355_T01 (Zea mays), 5'ss of exon 5
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat----gctttatgattttattactctggttccacttgtaaattcaccttctgatgttaaatacagtacttca--ttgtgtatccagtcttttccatc
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CTTTTGGTGGCTTTAAAAGTTCGATATCCTCAGAGGATCACCATTCTCAGAGGAAACCATGAAAGCCGGCAGgtatacaatttcttgtttgacagattgttcatgtttacttgatgcatcactccattctctgtaatcagctgtacaaactaaagtttttagtgaaattatttgcag-
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA09G15900.2 (Glycine max), 5'ss of exon 4
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgattttattactctg-gttccacttgtaaattcaccttctga---tgttaaatacagtacttcattgtgtatccagtcttttccatc
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CTTCTTGTGTCACTGAAAGTGCGATATCCTCAGCGAATTACTATTCTTAGAGGAAACCATGAAAGCCGTCAGgtatgcttaatcttctttcattcaaaattatgtattatgttcctgaggttcttttatcagacttttttatggagttattaact-tgtattctttaatgccg---
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA02G26650.1 (Glycine max), 5'ss of exon 5
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgattttattactctggttccacttgtaaattcaccttctgatgttaa-atacagtacttcattgtgtatccagtcttttccatc---
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CTTCTTGTGTCACTGAAAGTGCGATATCCTCAGCGAATTACTATTCTTAGAGGAAACCATGAAAGCCGTCAGgtatgcttgca-tgcaaaatcttctttc---gttcaaaattatgtattatgttcctgaggttcttatattggacttatttatggagttattaacttgtattcct
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G36510.1 (Glycine max), 5'ss of exon 5
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgatttt-attactctggttccacttgtaaatt-caccttctgatgttaaatacagtacttcattgtgtatccagtcttttccatc--
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CTCCTCGTGGCACTGAAAGTTCGGTATCCTCAGCGAATTACTATTCTTAGAGGAAACCATGAAAGCCGTCAGgt----ttgtgttttaaatctttcaaaactataaattactttctgaactgtagttatttgtgaatggcacataaattagctagtcttggaggctttgtatttgt
upper sequence: AT2G42500.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G39170.1 (Glycine max), 5'ss of exon 5
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagac----taatgctttatgattttattactctggttccacttgtaa--attcaccttctgatgttaaatacagtacttcat-tgtgtatccagtcttttccatc-------------------------------------------------------------------------------------------
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CTCCTTGTGGCACTGAAAGTTCGGTATCCCCAGCGAATTACTATTCTTAGAGGAAACCATGAAAGCCGTCAGgtttgtgttttaactctttcagaactataaattactttctgaactgtagttatttatttgtgaatggcacataaattagctagtctgggaggctttgtatttgtatgataaattgttgtttctaaacatttttggctgtgatttgaagacttgtatgggtggttgagctaattgttcctttatcatcctttaatgcagMapped 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|125191481|gb|EL206435.1|EL206435EST: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAG ATTACTCAGGTTTA
genomic: GATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaat ... catctcgcagATTACTCAGGTTTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGTTAGTCGCCTTAAAGATGCGATATCCTCAGCGAATCACTATTCTTAGAGGAAACCATGAAAGTCGTCAGgtagactaatgctttatgattttattactctggttccacttgtaaattcaccttctgatgttaaatacagtacttcattgtgtatccagtcttttccatc
- - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttttcc