Sequence
atgc intronic sequence ATGC exonic sequencegttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 2
gttgaaactttggcctactcaatcctattacactctt-tcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
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--tgtaagctacatctgtt-gatagatctgcacttcaatatatgttgcactcagtgcattttccttgaggtatgttca--tagatcttaattctcttcttttc-------agATCCTTTTTCTATGGCACCTCCTAAAGCCCTTGAGAGTATTGGAAAAACGTTGCATTCACAGTATGAGCGCTGGCAACCTAAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 2
gttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagt-caattttatctctattttttttctttctgatg--gcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
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------------gattaagtagaatttttgtgatgtatcaaaactgtag--atgcttgcaaaccatggtaacagtgcaaacagttttttatgcttacctttttcaataccgcagATCCTTTTTCTATGGCACCGCAAAAGGCATTGGAGTCAATTGGAAAAACTTTGAGCAGTCAGTATGAAAGATGGCAACCAAAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 2
gttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
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----------tgattaagtagaattt-ttgtgatctatcaaaactgtatatgcctgcaaccatggttacggtgcaaacagttttttatgcttacctttttcaatactgcagATCCTTTTTCTATGGCACCACAAAAGGCATTGGAGTCAATTGGAAAAACTTTGAGCAGTCAGTATGAAAGATGGCAACCAAAG
upper sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 2
gttgaaactttggcctactcaatcctattacactctttcttt-tctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
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------ttccttgacaaccagagagtagagtaaaaatagattgtattttttgagaaactggattagtcacttttgtcattttg----ctaatatttctcatact--ttgcagATCCATTTTCTATGGCTCCTCAAAGAGCACTGGAGATGATTGGAAAAAACTTGAGTGCTCAGTATGAAAGGTGGCAACCCAAGMapped 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|116460308|gb|EG502900.1|EG502900EST: GCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAG ATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATT
genomic: GCCGGATGTTATAAAGATATCTCCTTGTGCTAGAATCGAGGCATGGATAGgttgaaactt ... ctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
ttctgat putative branch site (score: 3)
tcaattttatctctat CT-rich tract
tcaattttatctctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaaactttggcctactcaatcctattacactctttcttttctgtgtttatcccttttttttgtcgccacagtcaattttatctctattttttttctttctgatggcagATCCATTTTCTATGGCACCGCCTAAAGCTCTCGAGACAATTGGAAAAAATTTGAGCACTCAGTATGAGAGATGGCAACCCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG