Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagtttttctcatttttttctgtgaactaataatagagaacacttaaaaccagcggcttagatatgaacaacttttacaattgtaatatgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09560.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 8
--------gtaaaagtttttctcatttttttctgtgaactaataatagagaacacttaaaaccagcggcttagatatgaacaacttttacaattgtaatatg-cagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
||| | | | || ||| | || || || || |||| |||| | | | | |||| | || ||||| || | ||| ||||| | |||||||| || || ||||| |||||||| || ||||| ||||||||||| ||||||| ||| | ||||| ||||
acaatcttagaaacacacattttagattcttccatagacctgaaactccatgttggtatcacagcaggctct----tgaa--attctaatttttgttctttggcagGACATTAAAGCACTTTTCCCTTCTGATTACAATCCATTTTATGCTGGATTTGGCAACAGAGATACAGATGAGCTTAGTTACAAAAAGATGGGAATTCCAA
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G05320.1 (Glycine max), 3'ss of exon 8
--------------gtaaaagtttttctcatttttttctgtgaactaataatag-agaacacttaaaaccagcggcttagatatgaacaacttttacaattgtaat-atgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
|||| | | | | | | | | ||| || ||| | | | || | | || | | || |||| | | ||||||||||||| | ||| |||||| | || || || || |||||||| |||||||| |||||||| |||||||| || ||||||||||| | |||||||| |
gtaactgccagaacacaaaaccatgccactgtgatgtataacagggaatgttattggaaggcatcttcttatcgacattataatacatatggcctaaaattattgttatgcagGATATCAAAAGACTTTTCCCATCTGACTATAATCCATTCTATGCTGGATTTGGCAATAGAGATACAGATGAACTTAGTTACAGAAAGATTGGAATCCCGA
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G19730.1 (Glycine max), 3'ss of exon 8
--------------gtaaaagtttttctcatttttttctgtgaactaataatag-agaacacttaaaaccagcggcttagatatgaacaacttttacaattgtaatatgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
|||| | || | | | | | | ||| || ||| ||| | | || | | || | | || | | | |||||||||||||| | ||| |||||| | || || || || ||||| || |||||||| |||||||| |||||||| || ||||||||||| | ||| |||| |
gtaactgccacaacacaaaaccatgtcactgtgatatataacagggaatgttattggaaggcttcatcttaccgacattataatacatatggcctaaattattgttatgcagGATATCAAAAGACTTTTCCCATCTGACTATAATCCATTCTACGCTGGATTTGGCAATAGAGATACAGATGAACTTAGTTACAGAAAGATTGGAGTCCCGA
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G35930.1 (Glycine max), 3'ss of exon 10
gtaaaagtttttctcatttttttctgtgaactaataatagagaacacttaaaaccagcggcttagatatgaacaacttttacaattgtaatatgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
|| || || | |||| | || | | || | | | | | || ||| || | || || | | ||||||||||||| | ||| ||||| | || || || ||||||||||| || ||||| ||||||||||| ||||| || |||||||| || | |||||||| |
------gtaatttccaaaacacacgc--aacttagaagtgccatcaaatgcatttatcatact-gacttga-cacatgttctgataatgttttgcagGATATCAGAAGACTTTTCCCTTCCGACTATAATCCGTTCTATGCGGGGTTTGGCAATAGAGACACGGATGAACTCAGTTACAGGAAGATAGGAATCCCGA
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0040g02800.t01 (Vitis vinifera), 3'ss of exon 7
--------------gtaaaagtttttctcatttttttctgtgaactaataatag-agaacacttaaaacc---agcggcttagatatgaacaacttttacaattgtaatat-gcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
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gttagtatgagaaggccgaacctcttaactgtatgtggaatggatgaattttagtaaaatgctcattctttcaaacaatttcataatttata--ttttaaaattatgtttttgcagGATATTAGAGCACTTTTTCCTTCTGATTACAATCCATTCTATGCTGGTTTTGGAAATAGAGACACAGATGAGCTCAGTTATAGGAAGATTGGGATCCCAAMapped 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|116396577|gb|EG439169.1|EG439169EST: TGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG GATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTC
genomic: TGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAGgtaaaagttt ... taatatgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacacttaaaaccagcggcttagatatgaacaacttttacaattgtaatatgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
ttttacaattgtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagtttttctcatttttttctgtgaactaataatagagaacacttaaaaccagcggcttagatatgaacaacttttacaattgtaatatgcagGATATCAGGAAACTCTTCCCAACGGATTACAACCCGTTCTATGCCGGATTTGGAAATAGAGACACAGATGAGCTGAGTTACAGAAAACTCGGAATCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA