Sequence
atgc intronic sequence ATGC exonic sequencegtgagttctttagaccttctttgtgtaattgatgattgagttgagcaatatgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23300.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G34890.2 (Glycine max), 3'ss of exon 2
---------------------------gtgagttctttagaccttctttgtgt-aattgatg------attgagttgagcaat-----atgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
|||| ||| ||| ||| | || | | | || || | |||||| | | || | || | ||||| |||||||||||| || ||||| |||||||| | || || ||||| |||||||||| ||||||||||||||||| |||||||||||||| ||||
gtgagttaaattaagattttgaaatgaaaaagttttttgttttcccttcatgttagtttctagtttttactacttttgacacccttcaacttgtttatactcttcttttaacttttttaagGTCTGTGATGATCGATTATCCGAGCTGATTCCTTGTCTGGACAGAAATCTCATATACCAAACAAGATTGAAGCTTGATTTATCTTTGATGGAGCACTATG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtgagttctttagaccttctttgtgtaattgatgattgagttgagcaatatgtg--tttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
| | |||| | | || | || ||| | |||| ||| || |||||| ||| | |||| ||| ||||| ||||||||||| | ||||||||| ||||| || |||| || ||| | |||||||||| ||||||||||||||| || | ||||||||||| ||||
gtgagttatcttagtctgaactgaacaacttttacatttatcctttccaataaccatgaatg-ttaatgtctagtgtgaggcataagttattttaatcttgcattcaatt--tgttaagGTCTGTGATGATCGTCTCTCGGAGCTAATTCCATGTCTAGACAGAAATTTCATATACCAAACAAGATTGAAGCTTGATCTGACGTTGATGGAGCACTATG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 1
---------------------------gtgagttctttagaccttctttgtgtaattgatgattgagttgagcaatatgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
|||| | | || | || | | || ||| ||| || || | | |||| | || ||| ||| |||||||||||| || ||||| |||||||| | || || || || |||||||||| ||||||||||||||||| |||||||||||||| ||||
gtgagttaaattaagattttgaactgaacaagttttatgttagtttctagtttctactactatgacacccttcaacttgt-ttaaactcttcttttaacttttttaa-gGTCTGTGATGATCGATTATCCGAGCTGATTCCTTGTCTGGACAGAAACCTCATATACCAAACAAGATTGAAGCTTGATTTATCTTTGATGGAGCACTATG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G00550.1 (Glycine max), 3'ss of exon 1
-------gtgagttcttta-gaccttctttgtgtaattgatgattgagtt----gagcaatatgtgtttaatattgttgttaattct------tgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
||||| | | | | ||| | | | || | | || | |||| || ||| || | | ||||| ||||||||||| || || ||| | ||||| |||||||| || ||||||| || ||||||||| ||||||| ||| | ||||||||||| || ||||
tcccttatctagttcaaggtggtgcatatcatacagatgaggctctacttttggaaatatcatcaatctaatggaatttgcaatgcttctgtttttgaagGTTTGTGATGATCGTCATTCAGAGTTGATTCCCTGCTTAGACAGACATCTTATCTATCAAATGAGACTGAAGCTGGATCTTTCTTTGATGGAACACTATG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G32470.1 (Glycine max), 3'ss of exon 2
--------------gtgagttctttag-accttctttgtgtaattgatgattgagttgagcaatatgtgtttaatatt---gttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
||||| | | | | ||| | | | || | | | || | | | || |||| || || | ||||| ||||||||||| || || ||| | ||||| ||||||||||| ||||||| || |||||||| ||||||| || ||||| |||||||||| ||||
ataagtagacacaatcaagttcatgggcatcatctaaatatggctatacttttggctcatcagcagtctcatggtgtttacaatgtttatgtttttgaagGTCTGTGATGATCGTCATTCAGAGTTGATTCCCTGCTTAGATAGACATCTTATCTATCAAATGAGGATGAAGCTGGACCTGTCTGTGATGGAGCACTATG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G04370.1 (Glycine max), 3'ss of exon 1
-----------------------------------gtgagttctttagaccttctttgtgtaattgatgattgagttgag-caatatgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
| |||| | | ||| | ||| || | |||| || ||| | | || | |||| || | ||||| ||||||||||| | |||||||| ||||| || |||| || ||| | |||||||||| ||||||||||||||| || |||| |||||||| || |
gtgagttatcttagtctgaactgaacaacttatacatttaccctttccaatagccttgaatg-ttggtgtctagtatgagtcattatagttattttactcttgtattcattttttaagGTCTGTGATGATCGTCTATCGGAGCTGATTCCATGTCTAGACAGAAATTTCATATACCAAACAAGATTGAAGCTTGATCTGACTTTAATGGAGCACTACG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 2
--------------gtgagttctttag-accttctttgtgtaattgatgattgagttgagcaatatgtgtttaatatt---gttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
||||| | | | | ||| | | | | || | | | || | | | || |||| || || | ||||| ||||||||||| || || ||| | ||||| ||||||||||| | ||||| || |||||||| ||||||| || ||||| |||||||||| ||||
ataagtgggcacaatcaagttcatgggcatcatctaaatatgactatacttttggctcatcagcagtctcatggtgtttgcaatgtttatgtttttgaagGTTTGTGATGATCGTCATTCAGAGTTGATTCCCTGCTTAGATAGACACCTTATCTATCAAATGAGGATGAAGCTGGACCTGTCTGTGATGGAGCACTATG
upper sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------------------------gtgagttctttagaccttctttgtgtaattgatgattgagttgagcaatatgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
||| || |||| | ||| | || | | || || | || || | || || || | | || | ||||| ||||||||||| || || || | ||||| ||| ||||||||||||||||||||||||||||||||||||| ||| | |||||||||||||| ||||
gtaagtttctagtagctgagctggaatcagcaccagtactagcctcctcttctctttgacactttgacttgtttatttttgcttcttatattcagt--tttcttttattgatg---gtgtcatgtttctgcttctgattttgaagGTTTGTGATGATCGGCATTCTGAATTAATTCCCTGCCTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGMapped 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|125236703|gb|EL250788.1|EL250788EST: TTTATGTAGAAGATGTAGTAGGGAATGGTTTCACTCCCAGAAGCTTTCCT GTGTGTGATGATCGACACTCGGAGCTTATTCC
genomic: TTTATGTAGAAGATGTAGTAGGGAATGGTTTCACTCCCAGAAGCTTTCCTgtgagttctt ... tcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgatgattgagttgagcaatatgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
tgttaat putative branch site (score: 3)
ttcttgt CT-rich tract
aatatgtgtttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttctttagaccttctttgtgtaattgatgattgagttgagcaatatgtgtttaatattgttgttaattcttgtaaagGTGTGTGATGATCGACACTCGGAGCTTATTCCTTGCTTAGATAGGAATCTTATATACCAAATGAGATTGAAGCTTGATTTGTCTTTGATGGAGCATTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA