Sequence
atgc intronic sequence ATGC exonic sequence...acagaatcagatcttggggttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G59290.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
--acagaatcagatcttggg-gttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
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ttataaacagggattttgtctgaaagaatcccttagtctgc-ataacttaatttttcttgatgccttgtttaa-ccaacatttctttcattc-ttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 3
acagaatcagatcttggggttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttactt-----ttttcttgtttgttttgtg-tagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
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------tttgtgaatgtggcttttgcagaagcaactattttgcatgagcctcttttttcttgtcttgatgccttgtttaccagtattctttcattcttgataatagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 3
acagaatcagatcttggggttttattagtt-tgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagC---CCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
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---caattgaatattgcttttgcagaagcaactattttgcataagcctctttttcttgtattgatgcctt-gtttaccagtatttctttcattcttgataacagTCCAACATGAGAATCTTGGTTACTGGAGGAGCTGGATTCATTGGGTCTCACTTAGTTGACAGATTGATGGAAAATGAAAAAAATGAG
upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
--acagaatcagatct-tggggttttattagtttgatctgttgtgactca-aggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
| |||| || || || | | | | | ||| | || ||| ||||| | | | | |||| ||| | | || |||||||||| || ||| || ||||||||||||| ||||||||||| || ||||| || ||||| ||||||||||| |||||||||
tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatctttaactaattcc-tacagtaattcctttcactcttgatg---gcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAG
upper sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------acagaatcagatcttggggtttta---ttagtttgatctgttgtgactcaaggatgattatg---taattatatgagtttacttttttcttgt-ttgttttgtgt-agCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
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gtaagcacgcaaatcaattcttggccagacctaattggtggaagttatgtagtccaggtttaaaacggtggttgtgattcatcgtaaactgttattactacctccagctttaactgcttttttagaagttgtgcatcgtcgtgactcagtcttgttgatttaaatatttgaggtatttttccgtttcagGCGAAGATGAGGATCTTGATCACAGGAGGAGCTGGATTCATCGGGTCTCACTTGGTCGACAGGCTCATGGAAGAGGGCACAAACGAAMapped 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|86047698|gb|DR343453.1|DR343453EST: CAAAGCCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTGTCAG CCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCAC
genomic: CAAAGCCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTGTCAGgtaaaatctt ... ttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCAC
EST:
gi|125053678|gb|EL124682.1|EL124682EST: CCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTTTGTCAG CCCAATATGAGGATCTTGATCTCTGGAGGAAGCTGGCTTCATTGGTTCTC
genomic: CCTCCTCCTTCTCCTTCTCCTCTCCGCAATTCCAAGTTTT-GTCAGgtaaaatctt ... ttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGA-GCTGGCTTCATTGGTTCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
tttacttttttcttgt CT-rich tract
attatgtaattatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acagaatcagatcttggggttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
- agaatca
- - - - - - - - -ggtttta
- - - - - - - - - - - - - agtttga
- - - - - - - - - - - - - - - - - - - - - actcaag