Sequence
atgc intronic sequence ATGC exonic sequencegtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79990.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
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-------------------------------------------------gtt--tattcaaatttcagagttcagtcttcggatctgaa-gttttgt--aattagtgctaatata-ttacctgcatcctaa--tcaaaatacttgattttatggtagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
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------------------------------------------------tgtt--tattcaaatttcagagttcagtcatcggatttgaa-gtttggtaatagtggtaatatattac----ctgaatcctaa--tcaaaattcttgattttatggtagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 6
gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggttt---aaattgttttcctaaattcacgcattcctacttttctgat-tctcgacttcaaaatcctgttcgtttt---gtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
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----------------------------------------------------------------tctatctgcatatggtgttttcttggctttcattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttacttgtttttacactagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGAMapped 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|124896506|gb|EH972720.1|EH972720EST: GAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAG CGTGGCACACTTTTTGGAGTCACGTGGCA
genomic: GAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaat ... gttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
ttctgat putative branch site (score: 3)
ttcgtttt putative PPT
ttcaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCATGACAGAAGATGCTCTAGAAGTAGCAACTGATCCTGACTACAGATTTGAGTTGGCCATACAGCTCGGTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC