Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcctgagggagcgaataattttaaaagaatatgattgagagagtgagagtgtgtttttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G02460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 2
------------------gtatgtcctgagggagcgaataatt-ttaaaagaatatgattgagagagtgagagtgtgtttttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
|| | | || | || | | | | || | | | | | | || |||| || | |||| || | || | | | | |||||||||||||||||| || ||||| || ||||| ||||| ||||||||||| ||||| ||| |||| || | ||| |
acttttgtaatgcatctagtttacttttgtaaagtgggtactggcttactgtgcattacttcactaacctcacagctgacatatttttgggtaaccatagGGACGGAAGGAGGATAAAAAAATGGAGGAAGATGATAGGTGTTGGTGGTAGTGACTGGAAACATTATGTTAGAAGAAACCCTCATGTGGTTAAAAGAAGA
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G047223_T03 (Zea mays), 3'ss of exon 2
--------------------gtatgtcctgagggagcgaataattttaaaagaatatgattgagagagtgagagtgtgtttttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
|| | | | | | | | | | || | | || | | | | | | ||| | || | | | |||||| ||||| |||| | | |||||||||||||||||||| || ||||| || | ||| ||||||||||||||||| || || ||| |||| || | ||||||
acttgtgtaaatcagttattgtcttacttcaccttcctatttctctaaataaactaccttacaagtgcttttattctatttcttttttatgttg-ctatagGGAGGAAAGAAGGATAAGAAAATGGAGGAAGATGATAGGTGTTGGTGGTAATGACTGGAAGCATTATGTTAGAAGGAACCCTCATGTGGTTAAAAGGCGA
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 1
---------------------------------gtatgtcctgagggagcgaataattttaaaagaatatgattgagagagtgagagtgtgtt----tttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
| ||| | | |||| | | || || |||||| || || | ||| || ||| | | ||||| |||||||||| ||| ||||||||||||||||||||||||||||| || ||||| |||||||||||| | |||||||||||| ||||||| | |
gtatttttgtttttcacctgttgatttgtgtttttctgtgttttaagcatgaatgagtatataa-aatatggcc-agtgattttacctgtattaccatttacctctcatcagATATAGGGAGGAGAGAAGGGTTAGAAAATGGAGGAAGATGATTGGGGTTGGTGGCAGTGACTGGAAGCATTATTTAAGGAGAAAACCTCATGTTGTTAAA------
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 2
---------------------------------gtatgtcctgagggagcgaataattttaaaagaatatg---attgagagagtgagagtgtgtttttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
| ||| | | || | | | ||||| ||| || |||| | | | ||| | || ||||| |||||||||| ||| ||||||||||||||||||||||||||||| || ||||| |||||||||||| | |||||||||||| ||||||| | |
gtatttttgttttacacctattgatttgtgtttttctgtgttttaagcatgagtgagtataaaa-aatgtggccattggttttacctgtatttccatttacctctcattagATATAGGGAGGAGAGAAGGGTTAGAAAATGGAGGAAGATGATTGGGGTTGGTGGCAGTGACTGGAAGCATTATCTAAGGAGAAAACCTCATGTTGTGAAA------
upper sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtatgtcctgagggagcgaataattttaaaagaatatgattgagagagtgagagtgtgtttttgt--------tgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
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ttttgcaaaatggagtttttttggctgtgtttgtgtatgtttttctcttgctataagcattaccggatattttactacaagacataaggtcctttttcagGGAGGAAAGACGGGTTAGAAAATGGAGGAAAATGATTGGAATTGGAGGGAGTGATTGGAAGCATTACGTTAGGAGGAAACCTAATGTGGTTAAAAGACGTMapped 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|125289632|gb|EL303717.1|EL303717EST: GTTTTAGCAAGTCTAAAACTACATCATCCACTGATCATGACAG AGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAG
genomic: GTTTTAGCAAGTCTAAAACTACATCATCCACTGATCATGACAGgtatgtcctg ... ctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaagaatatgattgagagagtgagagtgtgtttttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
aatatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcctgagggagcgaataattttaaaagaatatgattgagagagtgagagtgtgtttttgttgttggctatctatagAGAGGAGAGAAAGGTGAGAAAATGGAGGAAGATGATTGGGGTTGGAGGGAGTGATTGGAAGCATTATGTTAGGAGAAAACCTAATGTTGTCAGAAGGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA