Sequence
atgc intronic sequence ATGC exonic sequencegtattcttgcaatctttaagaaatttaagtttggtttttgtggggtcatggcatatcttattggatgtattacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02180.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g02850.2 (Oryza sativa), 3'ss of exon 5
-----------------gtattcttgcaatctttaagaaattt---aagtttggtttttgtgg-ggtcatggcatatcttattggatgtattacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
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gtattgagagcatatttcaatacatagaattacacaaagttttgctacctttcctttttgaagtacttttggaatgatctgatctttgcatgattttcagATAATACTTTGGATGGCGTTGTGGTGGAAACCAGTTCGAGCAATGGTCATCTTGTCTAAGATGTTCTTTGCAG
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g39220.1 (Oryza sativa), 3'ss of exon 5
-----------------------gtattcttgcaatctttaagaaatttaagtttggtttttgtggggtcatggcatatcttattggatgtattacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
|||| || | | || ||| | || | | |||| || || | || ||||||| ||||| ||||| ||||| | |||||||| || |||||||||||| | ||| | || ||||||||||||||||
ggaatgcaatccatctgtcttatctatttctgagctaacacatgaaaacaaggagcatattgcttacg-catgaaatgatttgatt-attcattactttcagATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G174286_T03 (Zea mays), 3'ss of exon 6
-----gtattcttgcaatctttaagaa---atttaagtttggtttttgtggggtcatggcatat-----------cttattggatgt--attacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
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aaatagtcacactgggcttgttgtgaatgcatttttatttgatacacgtaaaataggaacattctggtttctggactcatttgacaccaatgaatttcagATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAG
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G003076_T03 (Zea mays), 3'ss of exon 5
-------------gtattcttgc--aatctttaagaaatttaagtttggtttttg-tggggtcatggcatat---cttattggatgt--attacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
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taaaaactggataataatcacactgggtttgtagtgtattcatttttatttgatactgacattctggtttctggactcagttgacatcaatgtatttcagATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAG
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 5
---------------------------------gtattcttgc--aatctttaagaaatttaagtttggtttttg-tggggtcatggcatat---cttattggatgt--attacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
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tcttgagtctgatctcggagtaaaaactggataataatcacactgggtttgtagtgtattcatttttatttgatactgacattctggtttctggactcagTTGACATCAATGTATTTCAGATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAG
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G003076_T04 (Zea mays), 3'ss of exon 5
-------------gtattcttgc--aatctttaagaaatttaagtttggtttttg-tggggtcatggcatat---cttattggatgt--attacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG---------------------------
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taaaaactggataataatcacactgggtttgtagtgtattcatttttatttgatactgacattctggtttctggactcagttgacatcaatgtatttcagATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAGGTATTCCATGTTTCATTAATTCATTTC
upper sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------gtattcttgcaatctttaagaaatttaagtttggtttttgtggggtcatggcatatcttattggatgtattacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
||| ||| ||||| | | ||| | | || || || | || | || || | | || ||||||||| | ||||| ||||| |||||||| ||| | | | | || | |||||||||||||||||||||||||
tgctacgaacatagccattattacttgtacagctgctttctttttgtgtataaagatga----tggtaatttcttgac-taccacttttcttgaactgttttcagATTGCTATGTGGTTTGTTTTATGGTGGAAACCTATCCCAATCGTGTTCATCCTATCTAAGATGTTCTTTGCAGMapped 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|19877197|gb|AU238028.1|AU238028EST: GACTCAGGCCAAGCTTCTTCACAATTAATGCAGTTGTATATGTAGTTCAN ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCNGTTCGAGTTATGGNAATC
genomic: GACTCAGGCCAAGCTTCTTCACAATTAATGCAGTTGTATATGTAGTTCAGgtattcttgc ... ttacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagtttggtttttgtggggtcatggcatatcttattggatgtattacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
ttacttcc CT-rich tract
atatcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcttgcaatctttaagaaatttaagtttggtttttgtggggtcatggcatatcttattggatgtattacttccagATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG