Sequence
atgc intronic sequence ATGC exonic sequencegtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G19190.1 (Glycine max), 3'ss of exon 2
gtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
|| | | || ||||| || | | | | || | || | | | | | | || | | || | | | ||| |||| | | | | || || ||| || |||||| |||| | |||||||||| || ||||||||||||||||| |||||| ||||| | ||||| | ||||| |||| || || ||||| | | |||
--gttagtagcatggacttaccaatttaattggtttattgttcatcacttaagttcttgtgcatgttat-----tcttatgatcttatcacttaatttgtactcttggttttgcccaaaagttaataaatctatcaattttgccatg-ttgttt--------agGTTCGACTGGATCCTTCTAGACCTTTGAGCAAGCATAAACATTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATACGTTCCACCCTCCACCCCTG
upper sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G43720.1 (Glycine max), 3'ss of exon 1
gtattttccccttcattttttgaatttgatatac-atttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
|| | |||| || || ||||| | | || | || || | | || || | | || | || | ||| |||| | | | | || || ||| || |||||| |||| | |||||||||| |||||||||||||||||||| || ||| ||||| | ||||| | ||||| |||| || ||| ||||| | | | |
----------gttagtagcatgaacttacaattttatttggtttattcttcatcactt----aaattcttgtgcatgtt--attcttatcacttgatttgtactctaacttttgcccaaaagttaatgaatctatcaattttgtcatg-ttgttt--------agGTTCGACTGGATCCTTCTAGGCCTTTGAGCAAGCATAAACACTGGGTTGTTGCTGAAATTCTTAAGAAGGCACAGATATATGTTCCACTGTCCACGCCAG
upper sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G31470.1 (Glycine max), 3'ss of exon 2
gtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
| | ||| | | | |||| | ||| || || ||| | || || |||| | || | | || ||||| | |||| |||||||||| ||||||||||| |||||||| |||||| ||| | ||||| | ||||||||||| || ||| ||| | | | |
--------------------------------------------------gttagtttcattgattcttttgtgtattgtgcttttggcatgattggtt--ctactctgggttttgcaagatggcttattgagtggctgcttttgtgattgtt----gttgcagGTTCGGCTGGATCCTTCTAGGCCTTTGAGTAAGCATAAACATTGGGCAGTTGCTGAAATTCTCAAGAAAGCACGTATATATGTTCCGCCCTCAATGCCAG
upper sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0070g00270.t01 (Vitis vinifera), 3'ss of exon 1
gtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
| || | | | | | | | || || | |||| ||| || || || | | || |||||| || || |||| | ||||||||||| ||||| ||||||||||| ||||||||| ||||| | ||||| | |||||||| || || ||| |||| | || ||
------------------------------------------------------------gtcagttgttaaagcaatcggttccttcctttc----tccactt--ctgctttttcataa------tggataaaataacttgtgaaacaacattatcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCTGAAATTCTGAAGAAAGCTCGAATCTATGTGCCACCTGAACCTATTG
upper sequence: AT3G18880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv09s0070g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
| || | | | | | | | || || | |||| | |||| || || | | || |||||| || || |||| | ||||||||||| ||||| ||||||||||| ||||||||| ||||| ||||||| | ||||||||||| || ||| |||| | || |
------------------------------------------------------------gtcagttgttaaagcaatgggttccttcctttc----tccactt--ccgttttttcataa------tggataaaataacttgtgaaacaacactgtcattccagGTTAGGTTGGATCCTTCTAGGCCCTTGAGCAAGCACAAGCATTGGGTTGTTGCAGAAATTCTGAAGAAAGCACGAATCTATGTGCCACCTGAACCTATTAMapped 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|19799256|gb|AU230546.1|AU230546EST: CCAAGTTCATGGCTCACGATGAAAA-GACTCCTGTAACATCGGCGATCGA GTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTT
genomic: CCAAGTTCATGGCTCACGATGAAAAGGACTCCTGTAACATCGGCGATCGAgtattttccc ... gaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTT
EST:
gi|19878428|gb|AU239259.1|AU239259EST: CCAAGTTCATGGCTCACGATGAAAAGGACTCCTGTAACATCGGCGATCGA GTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTT
genomic: CCAAGTTCATGGCTCACGATGAAAAGGACTCCTGTAACATCGGCGATCGAgtattttccc ... gaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
acttgat putative branch site (score: 5)
ttgtttgaaatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattagGTGAAATTGGATCCTTCAAGGCCTTTGAGCAAGCATAAGCATTGGATTGTTTCAGAAATCATAAAGAAAGCACGCATTTATTCTCCACAAGCTGCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT