Sequence
atgc intronic sequence ATGC exonic sequenceCAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat...
Basic information
species | Arabidopsis thaliana |
transcript | AT1G75330.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 5'ss of exon 2
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgag---------tttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat
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TGATGATATCCAGATGGGCAAGCGTGAAGAGACCCGTGATGTTGCTCGTGTGCTTTCTGGATATAATGACATCATTATGGCCAGGGTTTTTGCTCACCAAgtatgatcataaggccctggcttttctgtttgatctgtttaccggcacaatctacttgtacacagatacagaatttacccta--cacataaa---atctgcatgc----
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 3
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtt-tttgattgattaataagggaacattagaagtgtacaaacatttcta-tggcttgttctaatctcagaaagataactgcattctcat--
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AGATGATATCCAGATGGGCAAGCGTGAGGAGACTCGTGATGTTGCTCGAGTACTTTCTGGCTATAATGATATCATTATGGCCAGGGTCTTTGCTCATCAGgtttggtcatgagttgtatgattaa--gatttcttttttgtgtttttttaccaacataaccaacaaggacatataatct--ggatcgtttctttttacatattt
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G349547_T01 (Zea mays), 5'ss of exon 2
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat-
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--ATGATATCCAGATGGGCAAGCGTGAGGAGACTCGTGATGTTGCTAGAGTACTTTCTGGCTATAATGACATCATTATGGCTAGGGTCTTTGCTCACCAAgtatggtcatgagttgcataattaagatttcttttatgtggtctttttaccaacataaccaacaat-gtcacataacctggatcatttttctttttacata
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G050371_T01 (Zea mays), 5'ss of exon 2
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttc-taatctcagaaagataactgcattctcat-
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AGATGATATCCAGATGGGCAAACGTGAGGAGACTCGTGATGTTGCTAGAGTACTTTCTGGCTATAATGACATCATTATGGCTAGGGTCTTTGCTCACCAAgtatggtcatgagttgcataattaagatttcttttatgtggtctttttaccaacataaccaacaagggcacataacct--ggatcatttttctttttacata
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G062142_T01 (Zea mays), 5'ss of exon 4
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttc-taatctcagaaagataactgcattctcat
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AGATGATATCCAGATGGGCAAGCGTGAGGAGACTCGTGATTTTGCTAGAGTACTTTCTGGCTATAATGACATCATTATGGCTAGGGTCTTTGCTCACCAAgtatggtcatgagttgcataattaagatttcttttatgt-ggtcttttaccaacataaccaacaacagcacataacctggatcatttttctttttacatat
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G03360.1 (Glycine max), 5'ss of exon 2
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgat-tgattaataagggaacattaga--agtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat
| ||||||| || ||||| ||||| ||||| |||||||| ||||||||||| | || ||||||||||||||||||||||||||||| ||||||||| |||||||||||||| | || ||| | | |||| | | || || | || || | || | | | |||| || |||| |
CGATGACATCCAAATGGGCAAGCGAGAGGAGACTCGTGACATTGCTCGTGTTTTGTCTCGCTATAATGACATCATTATGGCTCGTGTTTTTGCTCATAAGgtatgctggtgaccggtgaatgtgacttactttatttcatttggccattggactacagttactcatgtttatggttagtgaagaattatctctgcctcta---
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G03280.1 (Glycine max), 5'ss of exon 2
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgat-tga-ttaataagggaacattaga--agtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat
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TGATGATATCCAAATGGGCAAGCGAGAGGAGACTCGTGACATTGCTCGTGTTTTGTCTCGCTATAATGACATCATTATGGCTCGTGTTTTTGCTCATAAGgtatgctggtgaccagtgaatgtgagttacttgtatttcatttggccattgtaccgcagttactcatgtttgtggtcagtgaagaattatatctgcatct----
upper sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 2
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat----------
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AGATGATATCCAGATGGGTAAACGGGAGGAAACTCGTGATGTTGCTCGTGTGCTGTCTTGTTATAATGACATCATTATGGCACGTGTTTTTGCTCATCAGgtatgctggtgagttttttaatgtttggtag-----tactcagatttca-----attggtcttgcatatgtgtatttaaagaaggtagatatattccacttctgttgcagMapped 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|124853062|gb|EH937499.1|EH937499EST: TATTTGCTCATCAG GACATTCTTGATTTGGCTAACTACTCGAGTGTACCAGTTGTCAATGGTCTG
genomic: TATTTGCTCATCAGgtatgctggt ... tcatttgcagGACATTCTTGATTTGGCTAACTACTCGAGTGTACCAGTTGTCAATGGTCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAATGACATTCAGATGGGTAAGCGGGAGGAAACTCGTGATGTTGCTCGTGTTCTTTCACGCTATAATGACATCATTATGGCTCGTGTATTTGCTCATCAGgtatgctggtgagtttttgattgattaataagggaacattagaagtgtacaaacatttctatggcttgttctaatctcagaaagataactgcattctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agggaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcattctc