Sequence
atgc intronic sequence ATGC exonic sequencegtaattccttgtgacatgttttttcagctttatctataattacattgcttggtttcattggtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21660.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G132060_T02 (Zea mays), 3'ss of exon 7
----gta-attccttgtgacatgttttttcagctttatctataatta----------cattgcttggtttcattg-gtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
||| || ||||| || | || | | | || | | ||||| ||||| || | | | ||| ||||| ||| | | ||| ||||||||||||||||| ||| ||||| | |||| || | ||||| ||||||||||||||||| ||||| |||||||||||||| || |||||||
gtacgtatgttttttgtgttataactgcaaagatagagcaattaccatccagatggtcattgtacggttttgatgtgataactcaccatgttcttaatttctactttattccaaa--gGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGC
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 4
------gtaattccttgtgacatgttttttcagctttatctata------attacattgcttggttt---cattggtttgtttacctaaaatctaatt----actatca-tttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
| || ||||| || | || | ||| || ||| || | || | |||| | ||| | | ||| ||| || || | | |||||||||||||||||| ||| ||||| | |||| | || | ||||| ||||||||||||||||| || || |||||||||||||| || |||||||
gtacgtatgcttttttgtgttataactgcaaagagccaaagatagagcaaataccatccagatgtctatgtatggttttggtgtgataacaccatattcttaacttccacttcgttcgacagGTTAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCATGAGCTTAAAGATGCTCTTGGTATGCCTGATGGTGCCCCTCCCCCATGGCTTATAAACATGC
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 8
gtaattccttgtgacatgttttttcagctttatctata-attacattgcttggtttcattggtttgtttacctaaaatctaattact--atcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
| | | | |||||| | | || || | | | | | | | | || || ||| |||| | || || |||| || |||| || | |||||| || | || ||| | || |||||||||||||||||||||||||| || |||||||| |||||||| ||||| ||||
-----ttttgctaagatgtttcccttgatctagttaagtgtcaagattatcagcacctataaaagttataacttggttcttattattttatataatgctgttcagGTAAAGTTGAGAGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATGCCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGC
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 8
----gtaattccttgtgacatgttttttcagctttatctataattacattgcttggtttcattggtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
| | | | | || || || ||||| || | | || ||| | | || | | | || | | || || |||| | |||| || ||||||| | |||||| || | | ||| | || || |||||||||||||||||||||||||| |||||||| || ||||| ||||| ||||
cctcctcaccagctttaatttggttgttagattttattta--agcatatcttttgactgaaaaggatcttatttttata---tgat-gtcattggttggtgcacagGTGAAGTTGAGGGAGATGAAACCTGGCATGCTATCACAGGAATTGAAAGAAGCTCTTGGTATGCCTGAAGGTGCTCCTCCTCCTTGGCTTATTAATATGC
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 4
gtaattccttgtgacatgttttttcagctttatctata-attacattgcttggtttcattggtttgtttacctaaaatctaattact--atcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
| | | | ||| || | | || || | | | | | | | | | || || ||| |||| | || || |||| || ||||||| | |||||| || | || ||| | || |||||||||||||||||||| ||||| || |||||||| |||||||| ||||| ||||
-----ttttgctaagatgcttcccttgatctagttaagtgtcaagattatcagcacctataaaatttataacttggttcttattattttatataatgctgtgcagGTAAAGTTGAGGGAGATGAAACCTGGCATGTTATCACATGAATTAAAAGAAGCTCTTGGTATACCTGAGGGTGCTCCTCCACCATGGCTTATTAATATGC
upper sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 8
--gtaattccttgtgacatgttttttcagctttatctataattacattgcttggtttcattggtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
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tactcaccagttttaattttgttattagattttattta--agcatatcttttgactgaaaaggatcttattttttta-tatgat-gtcattggttggtgcacagGTGAAGTTGAGGGAGATGAAACCTGGCATGTTATCACATGAATTGAAAGAAGCTCTTGGTATGCCTGAAGGTTCTCCTCCTCCTTGGCTTATTAATATGCMapped 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|125092986|gb|EL150748.1|EL150748EST: CTAAGCTGTCAGCTCTAGGCGATTTGTATTTTGAAGGGAAAGAATTTGAG GTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAAC
genomic: CTAAGCTGTCAGCTCTAGGCGATTTGTATTTTGAAGGGAAAGAATTTGAGgtaattcctt ... tgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtttcattggtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
atctaat putative branch site (score: 3)
taaaatctaattacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccttgtgacatgttttttcagctttatctataattacattgcttggtttcattggtttgtttacctaaaatctaattactatcatttgggaaatagGTTAAACTGAGGGAAACGAAACCAGGGTTTTTGTCAAACGACTTAAAAGAAGCTCTTGGTATGCCTGAAGGCGCTCCTCCCCCATGGCTGATTAACATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT