Sequence
atgc intronic sequence ATGC exonic sequencegtgagaaactagtactagtagtgctctttgcttgtttcccttacaagattattcaattgctgatccttggatgtttttctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59580.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------------------gtgagaa--actagtactagtagtgctcttt--gcttgtttcccttacaagattattc-aattgctgatccttggatgttttt--ctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
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gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
upper sequence: AT3G59580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G105004_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------gtga--gaaactagtactagtagtgctctttgcttgtttcccttacaagattattcaattg-ctgatccttg-gatgtttttctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
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gtgagccctactgtattgttacgaagtctctgttaaatctagatttgctgtgacattcacagtactgattactgaagataatgccatcattgtagaagaatttcttagattaggagattatggaatgaactgcttcttctgacacttgcctataaacaccatt---gcagTTTGTCCAACGACATTGAAACGAATATGCAGACAACATGGAATTTCCCGATGGCCATCTCGAAAGATAAACAAGGTCAATCGTTCATTGAAGAAGATAGA
upper sequence: AT3G59580.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------gtga-gaaactagtactagtagtgctctttgcttgtttcccttacaagattattcaattgctgatccttggatgtttttctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
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gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctg-acacttgcctataaacaccatt---gcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGAMapped 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|125227187|gb|EL241272.1|EL241272EST: ATGCTGCAAAAAGCCTTGGTG TTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGAT
genomic: ATGCTGCAAAAAGCCTTGGTGgtgagaaact ... ctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagattattcaattgctgatccttggatgtttttctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
tgctgat putative branch site (score: 3)
tgtttttctttttgct putative PPT
atgtttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaaactagtactagtagtgctctttgcttgtttcccttacaagattattcaattgctgatccttggatgtttttctttttgctttctttctgcagTTTGTCCGACTACACTAAAAAGGATATGTAGACAACACGGAATTATGAGATGGCCATCTCGAAAGATTAACAAAGTGAATAGGTCACTAAGGAAAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA