Sequence
atgc intronic sequence ATGC exonic sequencegtatttatttttgggcatgatagcatatattacgttctaaatttgaatcgtcattattactaatctgcgattgataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57410.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G180988_T01 (Zea mays), 3'ss of exon 4
gtatttatttttgggcatga--tagcatatattacgt-tctaaatttgaatcgtcattattactaatctgcgattgataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
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gtacacacttgtgaacttaaattctgttttattatgtgtactagttctagccttccttgtgactg-tctgt--------attgcagGATGAAGCTGGGACTGCAGCAATCAAGACAGTTGAACTTGATGCCATCCTTGGGGGTCGTGCAATCCAACATAGGGAACTCCAAGGTTATGAATCTGACA
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G047310_T02 (Zea mays), 3'ss of exon 4
gtatttatttttgggcatgatagcatatattacgttctaaatttgaatcgtcattattactaatctgcgattgataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
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gtacacacttgtgaacttaa-attccgtgtta--ttatatgtactagtc-ttagccttccttgtgactgtttgt--attgcagGATGAAGCTGGGACTGCAGCCATCAAGACAGTTGAACTTGATGCCATCCTTGGGGGTCGTGCAATTCAACATAGGGAACTCCAAGGTTACGAATCTGACA
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 4
---------gtatttatttttgggcatgat---agcatatattacgttctaaatttgaatcg-----tcattattactaatctg-cgattgataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
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aaagtgagtttatatatgatggttcacaatttggaaattcttgaaccaatatatttggatggaagaataatctctattgatatggtgattttccattt-agGATGAGGCTGGAACAGCAGCCATTAAAAATGTTGAACTCGATGCATCTCTTGGAGGACGTGCAGTGCAACACAGGGAAATTCAAGGGCATGAATCTGACA
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 3
--------gtatttattt--ttgggcatgatagcatatattacgttctaaatttgaatcgtcattatta----ctaatctgcgattgat---aattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
|| || | || |||| | | || || | | | | | ||| | | || || | || ||| | |||| | ||| ||||||| |||||||| ||||| | || || |||||||||||||| ||||||||||| || || || || | | ||||| ||||| ||||| || ||||
atttagatgtgttgagttatttggaaagggcaggggttaggagggttcatagttgctttgacaaaataataatcttggctgacactgattttacttctagGATGAGGCTGGAACTGCAGCCATTAAAACTGTTGAACTTGATGCTGCTCTTGGAGGGCGTGCAGTGCAGCACAGGGAAATCCAAGGACATGAGTCCGACA
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 3
gtatttatttttgggcatga---tag--catatattacg-ttctaaatttgaatcgtcatta-ttactaatctgcgat----tgataattcc------agGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
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ttttctctttctggttctaaagttggtttatgtatgatggttcaaagtttggaaattcttgaaccaataatctctattgatatggtgattttccttgtagGATGAGGCTGGAACAGCAGCCATTAAAACTGTTGAACTCGATGCGTCTCTTGGAGGACGTGCAGTGCAACACAGGGAAATTCAAGGGCATGAATCCGACAMapped 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|164010914|gb|EL990497.1|EL990497EST: CGCTTATCTATTTGATATACATTTTTTGGATTGGTAAAGATACAAGCCAG GATGAAGCTGGAACAGCAGCTGTCAA
genomic: CGCTTATCTATTTGATATACA-TTTTTGGATTGGTAAAGATACAAGCCAGgtatttattt ... ataattccagGATGAAGCTGGAACAGCAGCTGTCAA
EST:
gi|116482622|gb|EG525214.1|EG525214EST: GCGCTTATCTATTTGATATACA-TTTTGGATTGGTAAAGATACAAGCCAG GATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTT
genomic: GCGCTTATCTATTTGATATACATTTTTGGATTGGTAAAGATACAAGCCAGgtatttattt ... ataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attacgttctaaatttgaatcgtcattattactaatctgcgattgataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
ttctaaatttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatttttgggcatgatagcatatattacgttctaaatttgaatcgtcattattactaatctgcgattgataattccagGATGAAGCTGGAACAGCAGCTGTCAAGACAGTTGAACTTGATGCAGCTCTTGGAGGCCGAGCTGTCCAATATCGTGAAATTCAAGGTCATGAATCTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG