Sequence
atgc intronic sequence ATGC exonic sequence...cttgtggtataaccttttatttttcatttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G31430.1 (Glycine max), 3'ss of exon 2
-cttgtggtataaccttttatttttcatttgctcctttctg---gagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
| | | | | | || | |||| || | |||| ||||||| || |||| || | || ||| | ||| | |||||||||||| |||||||||||||| |||| || ||||||| || ||||| ||||| ||||| |||| |||||| ||||||||||| || ||||| |
ataaatagataagctgtgttttatctattttatctaaaatatacaagcagatagatttgtcagaatcatta--gtctaacaaaaatttgcgtgtttgggaa--gATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACTTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTATGTCT
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G31510.1 (Glycine max), 3'ss of exon 2
----cttgtggtataaccttttatttttcatttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
||| | | | || | | || || | | | || |||| || || |||| ||| | | | | | | | | | | ||||||||||||| |||||||||||||| |||| || ||||||| || || || ||||| |||| |||| |||||| ||||||||||| || | |||||
aacatgaatggatggtacatgttttctgtagtttcttataattaaaacatgtagacttgtcagaatcattg-gtccaacaataa---cttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTCCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
--cttgtg-gtataaccttttattttt-catttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
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aacatgaatggatgatacatggtttctgtagtttcttgtaattaaaacatgtagacttttcagaatcattg-gtctaacaatga---cttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G25010.1 (Glycine max), 3'ss of exon 2
----cttgtggtataaccttttatttttcatttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
| | |||||| | | | || | |||| ||||||| || |||| || || ||| | | ||| ||| ||||||||||||| |||||||||||||| |||| || ||||||| || ||||| ||||| | || |||| ||| || ||||||||||| || ||||| |
ataaatagataagctgtgttttatctattttgtgtaaaatatactagcagatagatttgtcagaatcatta--atctaacaaaaatttgtgtgtttg-aca-agATTCGTGATACGAGTGTTCTTGTGAGGTTGAGACCTGCATGGGAAGATCTTCGGAGCTACCTTACTGCAAGAGGACGCAAGCGTTTTGAGGTTTATGTCT
upper sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 2
cttgtggtataaccttttatttttcatttgctcctttctg-gagcacctagatttttctgaat-------tcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
||| | | || || | ||| | | | ||| || | | | || | | | ||| | ||| | ||| | |||||||||||||||||||||| |||||||| | || || |||||||||| || || ||||| | || |||| ||||| ||||||||||| || |||||||
--------ataccactatacttcttgtttatgtcatccaataagcctgtaaactcattccaagaaactggtttgtttagtgacacaaaatttttttatatctccacagATTCGTGATACAAGTGTACTTGTGAGGCTAAGACCTGCATGGGAGGACCTCCGGAGCTACCTAACTGCAAGGGGGCGCAAGCGTTTTGAGGTTTATGTTTMapped 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|125217312|gb|EL231395.1|EL231395EST: TTGCAAGAGAAGAATATTATTCTGACTCGCATTAACCCAATG ATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTT
genomic: TTGCAAGAGAAGAATATTATTCTGACTCGCATTAACCCAATGgtatgcaagt ... ttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
tatatttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtggtataaccttttatttttcatttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - cctttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatc