Sequence
atgc intronic sequence ATGC exonic sequence...aaattgggtttatgaggtttgtgttaagtgtggtgacagtagtgctagcgatctgattgagatatatgccacagtctggtgattttattggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02030.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g52770.1 (Oryza sativa), 3'ss of exon 1
aaattgggtttatgaggtttgtgttaagtgtgg-tgacagtagtgctag-cgatctgattgagatatatgccacagtctggtgattttattggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
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-tattgaaaaagt-agcatagtgggacacatgaatcagagtttagcttgtcaatttggatattggagagatgaatgcttacttctgttttgtgtttttttagGTGCAACAATCAAATCTGGAAGCTCTTTTACAGAGGCATGTGAAGATGGCCGCTGAGATCAAGAATCTGGATACAGACTTACAAATGCTAGTATATGAGA
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01610.1 (Glycine max), 3'ss of exon 1
--------------------aaattgggtttatgaggtttgtgttaagtgtggtgacagtagtgctagcgatctgattgagatatatgccacagtctggtgattttattggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
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gtgaattcttcttcccctcctctctcaattaatcactctcgtcgttttcgtcgtcgtcgtcgtcgtcgaagatgaacttcaatttggagcatgaatgaatgaat-----gaattatgcagGCACACAAGTCCAATTTGGAAGGCCTTCTACAACGCCACGTTGCAATGGCTGCTGAAATCAAGAATCTCGACACCGACTTGCAAATGCTAGTTTACGAGA
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G01660.1 (Glycine max), 3'ss of exon 1
--aaattgggtttatgaggtttgtgttaagtgtggtgacagtagtgctagcgatctgattgagatatatgccacag----tctggtgattttatt------------ggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
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gtaaattcttcttccccttctccctcaattagtcactctcgtcgaagtcgaagacgaacttgaatttggagcacgaaacctcacttgattttattaaatgaatgaatgaattatgcagGCACACAAGTCCAATTTGGAAGGCCTGCTCCAACGCCACGTTGAAATGGCAGCTGAAATCAAGAATCTCGACACCGACTTGCAAATGCTGGTTTACGAGA
upper sequence: AT4G02030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv07s0005g01440.t01 (Vitis vinifera), 3'ss of exon 1
aaattgggtttatgaggtttgtgttaagtgtggtgacagtagtgctagcgatctgattgagata----tatgccacagtc-tggtgattttattggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
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-----gaaggtaggggtccagcagtgagcttggtatccttgttgcttacctgtagttttctataatcttcttatataataatatttgcttcatttgtatgtgaagGCACAAAAATCAAATTTGGAAGGACTTCTTCAAAGACATGTTGAAATGGCAGCTGAGATAAAAAATCTTGACACTGACTTGCAGATGTTAGTGTATGAAAMapped 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|19876508|gb|AU237339.1|AU237339EST: ATAACATCAACAGCACTTCCTTTGATGCTGATCAGTACATGGATCTCATG ATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCT
genomic: ATAACATCAACAGCACTTCCTTTGATGCTGATCAGTACATGGATCTCATGgttagtcttc ... gcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagcgatctgattgagatatatgccacagtctggtgattttattggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
atctgat putative branch site (score: 4)
tgattttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattgggtttatgaggtttgtgttaagtgtggtgacagtagtgctagcgatctgattgagatatatgccacagtctggtgattttattggcttgtgcagATCAAAAAGTCGAATTTGGAGGTGCTTCTGCAAAGACATGTTCAAATGGCTGCTGAGATTAAAAATCTCGACACAGACTTGCAAATGCTAGTCTATGAAA
- - - ggtttat
- - - - - - - -ggtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacagtc