Sequence
atgc intronic sequence ATGC exonic sequence...atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagattcggattagaactgagttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03960.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 1
atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagattcggattagaactgagttcttctgt-------ttataatgtttc---agGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
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------tgctcctgcgctacatttttctgtgatgtataa----tatctgacagattcatgttagtatcagaagctagtttcttaacagcatcgctgttttgttttggtagGAATGAATAAGATGGTCATTAACCATCTCGACAAGCTCTTTGTCACGAACGATGCTGCAACAATTGTGAATGAGCTCGAGGTCCAGCACCCTGCTGCTAA
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 1
-------atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagattcggattagaactgagttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
||| || | | ||||| | | |||| ||| |||| ||| | ||| | |||| | || || | | | | ||||||||| || |||||||||||||| |||||||| |||||||||||||| || ||||| || || ||||||||||| ||| |||||||||||||||||||
ttttgcaatacgttttgtgtctgacaaaatttacttagatgctgaaacctt---ctagtgatcgactgcttgat---gtcgtagttttacttgtttttttatgt-agGAATGAACAAGATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATCGTGAATGAGCTTGAGGTTCAGCACCCGGCTGCTAA
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 1
---atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagattcggattagaactg-agttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
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gcgctatgtaaatcacatcggacaaacttttacttagatgctgaaaccttccagggatc--gatt--gcttgatgttgtagttctccgtgtttcctttttgtagGAATGAACAAAATGGTTATCAATCACTTGGACAAGCTGTTTGTCACAAACGATGCTGCCACCATTGTGAATGAGCTCGAAGTTCAGCACCCTGCCGCTAA
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 1
atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagatt--------cggattagaactgagttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
|| | | || || |||| ||| ||| || | ||| | |||| ||| | || | | | | | || ||||| || ||||||||||||||| |||||||| ||||| |||||||| || |||||||| || || |||| || || |||||||| || || ||||||| || ||||| ||
---gtgcttgta---ttaatatgttgctg--aagaatgcgtttgtttggatagatttagaatgttggtggtggtcttgttttcaaatgttttgtttgatctgattcagGAATGAATAAGATGGTTATAAATCACTTGGACAAGCTTTTTGTCACGAACGATGCTGGGACAATTGTGAATGAACTTGAAGTTCAGCATCCTGCTGCCAA
upper sequence: AT3G03960.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------------------atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagatt----cggatta---------gaactgagt-tcttctgtttata-----------atgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
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gtattccttttcatttctcatatgttgttctaactgggacctttttggagactttcgatcagttcgctgtgcattctatcttcttgttgagttgggaaaataattgatttttaaatcgcgctagatttgatcgggttatgtttgtaagaattgggtgttttttatttatttttatttttatgtgattcagGAATGAATAAGATGGTCATCAATCATTTAGACAAGATCTTTGTGACGAATGATGCTGCAACTATTGTAAATGAGCTTGAGGTTCAGCATCCTGCCGCCAAMapped 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|86067734|gb|DR363491.1|DR363491EST: AGCTTGCAAGGAGCTCTCCACCATTACTCGCACCTCTCTCGGTCCCAATG GAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATG
genomic: AGCTTGCAAGGAGCTCTCCACCATTACTCGCACCTCTCTCGGTCCCAATGgttcgtaatg ... aatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctagggattcagattcggattagaactgagttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
tgtttataatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atagtttaagcaagcttgatctgttactgtaaaggtgaagtctttttctagggattcagattcggattagaactgagttcttctgtttataatgtttcagGAATGAATAAAATGGTTATCAATCATTTGGACAAACTGTTTGTCACAAATGACGCTGCTACTATAGTGAATGAGCTCGAGATTCAGCACCCGGCTGCTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - -aagcaag
- - - - - - - - - - ctgttac