Sequence
atgc intronic sequence ATGC exonic sequenceGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtctcttagcctagaggattactcctgattatatgaatgacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 2
GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtctcttagcctagaggattactcctgattatatgaatgacag--------------------
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GTACAATCCATATGTGCAGGCCAGAAGCAGGATAGATCAGCTCAAAAGGCTAGGCCATAGTGTAGACAAGgtttgcccttacccttgagagtgttgtgt---cttggtttgagtaattcgattcactttctagttacatttgattaatgct-atcataagtttaaaataatttgaatacattatgcag
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 2
GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgtt-----agagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtct---cttagcctagaggattactcc----tgattata---tgaatgacag
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GTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAGgtttgtctggagtccaagacagcactcagctcaattttattgattcttatattcacgacatgctgtattaaattttgaccagcagttggagatgattataatgtacattgcag
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 2
GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagtttgatatttctagtaacctgtgagtatt---attttcgttctttttaccagtctc--ttagcctagaggattactcctgattat----atgaatgacag
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GTATAATCCATATGTCCAAGCGAGGAGCAGGATAGATCAGCTTAAGCGTTTGGGTCATAGTGTAGACAAGgtttgaagctcatttt----atatctcttgaatattccaatccaagtacatgaaatgagagtagatttactgtgtgaagtccttgtaactatggttgttgttttcag
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 2
GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagtttgatatttctagtaacctgtgagtatt---attttcgttcttt--ttaccagtctcttagcctagaggattactcctgattat----atgaatgacag
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GTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTTGGGTCATAGTGTAGACAAGgtttggagctcattttac----atctcttgaatattccaatccaagtgcatgaaataagagtagatttactgtgtaaagtacttataattatggttgttattttcag
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 2
GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagtttgatatttc-tagtaacctg--tgagtatt---attttcgttctttttaccagtctcttagcctagaggattactcctga-ttatatgaatgacag-----------
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ATATAACCCATATGTCCAGGCTAGAAGCAGGATCGATCAGCTGAAGCGGCTGGGTCATAGTGTAGACAAGgttt-agtttgttgtctggttataatctaattatttatttacagttgtgcaatacatcttgatttattggtaagcatacttgtttgcatcttgtttcaatggctgcatgttttcagMapped 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|301501204|gb|HO206744.1|HO206744EST: CAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG GTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTAT
genomic: CAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagttt ... tgaatgacagGTTGAGTTCATTTTGATGGGAGGTACTTTCATGTCACTGCCTGCTGAGTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAGgttagagtttgatatttctagtaacctgtgagtattattttcgttctttttaccagtctcttagcctagaggattactcctgattatatgaatgacag
- - - - - - - - - - AAGAAG
- - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - TGAAGC