Sequence
atgc intronic sequence ATGC exonic sequencegtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G11270.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 3
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
|| || | || |||| | || || | |||| | || | || || ||| | | | |||||| || ||||| |||||||| ||||| ||||||||||||||||| || || || || || || || ||||| ||||| || || |||||||| ||||||
------------------------------------------------------------------------------taaagttaattatgctagcttcgtcactgggtgctcctgctgtattgcctgtggcgcttctcacagctgttta-ttccaattctcgctctccaaattgcagTTATGTTCCTAATCCAGTCTTGGTGATTATTGATGTCCAACCCAAGGAGCTGGGTATACCGACCAAAGCGTACTACGCTGTGGAGGAGGTTAAAGAG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 3
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
| ||| | | | | || | | || | || | ||| | ||| | |||| || | | ||| || | |||||| || ||||||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | |||||||| ||||||||||| ||||| ||||| ||||| |||||
-------------------------------------------------------------------------tcttat-tctctttgcctctttatgtctttaacattttcatctgtagttttg-tgtacctgatcaatct-tta--tccatattaatcaagcttaaaactgttgcaGCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCTGTTGAAGAGGTTAAAGA-
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 3
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
||| | ||| | | || | |||| ||| | ||| | |||| || | | ||| || ||| || | | ||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | |||||||| ||||||||||| ||||| ||||| ||||| ||||||
--------------------------------------------------------------------------cttattctctttgcctctttctatc-tttatcatcttcatctgtagttttg-tgtacctgatcaatct-ttatccaaatt--gatcaagcttaaaactatcgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTGGGAATCCCAACAAAAGCATATTATGCCGTTGAAGAGGTTAAAGAG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 2
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
| || || | | | | ||||| | |||| | || | | | || | | ||| | || |||| | | || || | |||||||||| ||||||||||| || ||||| || |||||||| ||||||| ||| | |||||||| | |||| |||| |||| ||||| ||||| ||||||
---------------------------------------------------------------cttattctctttgcctctttctat---ctttaatgttttcatt-tgtagttttgtgtacctgatcaatctt-tatccaaattaatcaagcttaaaatt-----------gttgcagCTATGTTCCAAATCCTGTCTTGGTTATAATTGATGTTGAACCTAAGGAATTAGGAATCCCAAGAAAAACATATTATGTCGTTGAAGAGGTTAAAGAG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 3
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
| | | || ||| | |||| || || |||| | | || | | | ||||||| | | | | | ||| || | |||||| || || || ||||| || |||||||| |||||||||||||| ||||| || ||||| ||||| || || |||||||| ||||||||||||||||||
---------------------------------------------------------------------cagatcaattaaatactggcatttttaatgcttt--ggtctaa-tgaattggtttccctttcttctggtctgtatgatt---ggtctgttctccgt----aatattgcagGTATGTCCCCAATCCTGTTTTGGTCATAATTGATGTCCAACCAAAAGAGCTAGGAATTCCCACGAAGGCTTACTATGCTGTTGAGGAGGTGAAAGAG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 3
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttat-atatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
||| ||| | | || | || || || ||| || || | ||| || | | || || | | | ||| | | |||| | | |||| ||||||||| ||||| ||||| || || ||||| |||||||||||||| || || || ||||| ||||| || || || ||||| |||||||| |||||||||
-----------------------------------------------------------gtgatct---tggatcatcaaatatattgacatttctaa-caatggaaattgattttccttcatctggtcggtgtgattaat---------cagtttc--------tctttggttttgcagCTATGTTCCCAATCCTGTCTTAGTCATAATTGATGTCCAACCAAAGGAGCTAGGAATTCCCACCAAGGCTTATTATGCTGTTGAGGAAGTGAAAGAG
upper sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaa---tcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
||||| |||| | | ||| || | || ||| | ||| || || | ||| || || | || ||| | || || | || | | || | | |||||| |||| || ||||| || | | | ||| || ||||| || |||||||||||| |||| ||||||||||| || |||| || ||||| || |||||||| || ||||||||||| |||| || |||| |
gtaagtccaattttattctgaactctg---catgtcgtactatgtagatgtacgacgtggccgt--aactacttcatgtata-gtagttcttagaatgaatagaacttatacttggcaatatttgctacccctt-caagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTGMapped 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|19875108|gb|AU235939.1|AU235939EST: GGTCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCTTTATTCAATGG CTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCACCCTAAAGAACT
genomic: GGTCCTAAACTTCGAGAGAATGATTTGGATGTTCACGCTTTATTCAATGGgtaagaccaa ... ggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
ttttaat putative branch site (score: 3)
ttttaatcttagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaatcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG