Sequence
atgc intronic sequence ATGC exonic sequencegtcagagaagataacaacagaacacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01320.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 13
--------------------gtcagagaagataacaacaga--acacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
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tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgca-aatttgcatagcctaatt---tggaatttgctttcaaattt--cagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 14
----------------------gtcagagaagataacaacagaacacaaac-tgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
| | | || | ||| | | | | ||| | ||| || || ||| | || ||||| |||||||| || ||||||||||| ||||| | ||| || || ||||||||||| || || ||||| || |||||||| | ||| |||| | ||
gggatccctgttcacttgtgttgctattttgtgcctccgtagcatacagccacatgagttgcattcattcagcacgctgaagca-------tgtcaaaaaatttcagGAGGAGAACTTGTCTGCAATGAACACCGATCCTTGGTATTCGGCATATCACTACTCCCACCCACCTCTCGTCGAAAGGCTGCAAGCTCTTGAAGATTCAG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA09G39150.1 (Glycine max), 3'ss of exon 13
-----------------gtcagagaagataacaacaga--acacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
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attttcaattttcactttttattcttcctcgtgtcattttgtgcaagtagattttgtttctggtgatgggaagtaaaatg--ctctatatctgcatttt-cagGAGGAGAATCTGTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCTGTGCTGGACGAACCGG
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G47190.1 (Glycine max), 3'ss of exon 12
----------------gtcagagaagataacaacagaacacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG-
| | | | | | | | | | | || | || | ||| | | ||||| ||||| ||||| | ||||| ||||| || ||||| | |||||| ||||||||||| || |||||||| ||||||||||| | || | || | | |
ttttcaattttcactttttattcttcctcatgctattatgtgcaaggagattttgttcctggtgatgggaagtaaagtgatttatacctgcatttt-caggAGGAGAATCTTTCAGCTATGAATACAGATCCTTGGTACTCTGCTTATCACTATTCTCATCCTCCCCTTGTTGAAAGATTGGCCGCGCTGGACGAACCGGA
upper sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
----------gtcagagaagataacaacagaacacaa--actgttacct-caatttgtg---tcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
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acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCGMapped 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|164047437|gb|ES067576.1|ES067576EST: TCTAGTGAAACTACAG GAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCAC
genomic: TCTAGTGAAACTACAGgtcagagaag ... gattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
ttaaatggatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagagaagataacaacagaacacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA