Sequence
atgc intronic sequence ATGC exonic sequencegttagtatttgaagtcacatgtacataggaagtgaatatgtggtatgcgtttggtggtgccttgatttgtgagtgctgatgtagcttttattgatagATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06600.3 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 5
----gttagtatttgaagtcacatgtacataggaagtgaatatgtggtatgcgtttggtggtgccttgatttgtgagtgctgatgtagcttttattgat--agATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
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ggatatcactatcatctgagacatgcattcaaaatacttgtctatggc---tgatttgcattcttgcgtcttctaaattaaattgtttttttttgtgatgtagATAAATGACCGTTATGAGTTCCCACTTCAATTGGATCTTGATAGAGATGATGGAAAATATCTTTCTCCAGACGCGGATAGAAGTGTGCGTAACCTATATA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 9
-gttagtattt--gaagtcacatgtacataggaagtgaatatgtggtatgcgtttggtggtgccttgatttgtgagtgctgatgtagcttttattg-atagATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
|||||||| ||| | | | | | | | || | | | | | ||| || | || | ||| ||| |||||||||| || ||||| || || ||| |||| || ||||||||||| ||||||| ||| |||| ||||| || || |||||||| ||||||||||| |
taatagtatttatgaaattctaaaaaatctagtgccatgtgtctctgat-tactgtatacttcatctttttcctagcaataataatggctttgttgtgcagATAAATGACCGTTATGAATTCCCTCTTCAACTTGACCTTGATAGAGAGAATGGAAAATATTTGTCACCTGACGCAGATAGGAGTGTTCGCAACCTTTACA
upper sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S42_181V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------gttagtatttgaagtcacatgtacataggaagtgaatatgtg-gtatgcgt-ttggtggtgccttgatttgtgagtgctgatgtagcttttattgat---------------------------agATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
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gtgaggaaaggggttttcgaaccatgcaatatgcaacattcggctggtatagcttatgtattgattgtgcatattatttagatgaaggacgtgtgtgtgtgtgtgtgtgtatttgctttgttttggttggttggtagtcacttttttactactgattacctttgaacattatttatgtgatgcagATTAATGATCGCTATGAGTTTCCTCTGCAACTAGACCTGGATAGAGAGAATGGAAAATATCTCTCTCCTGATGCTGACCGCAGTGTGCGAAATTTATACAMapped 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|124711076|gb|EH802478.1|EH802478EST: TCCAGCTCAAGAGGTTTGAATATGACTTTATGAGGGACACCATGGTGAAG ATAAATGATCGGTA
genomic: TCCAGCTCAAGAGGTTTGAATATGACTTTATGAGGGACACCATGGTGAAGgttagtattt ... ttattgatagATAAATGATCGGTA
EST:
gi|124744738|gb|EH835900.1|EH835900EST: TTTGAATATGACTTTATGAGGGACACCATGGTGAAG ATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGAT
genomic: TTTGAATATGACTTTATGAGGGACACCATGGTGAAGgttagtattt ... ttattgatagATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgcgtttggtggtgccttgatttgtgagtgctgatgtagcttttattgatagATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
tgctgat putative branch site (score: 3)
cttttatt putative PPT
ttttattgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtatttgaagtcacatgtacataggaagtgaatatgtggtatgcgtttggtggtgccttgatttgtgagtgctgatgtagcttttattgatagATAAATGATCGGTATGAGTTTCCGCTTGAACTGGATCTTGATAGAGAAGATGGAAAGTATCTGTCGCCTGATGCTGACAGGAGTGTCCGCAACCTTTATA
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