Sequence
atgc intronic sequence ATGC exonic sequencegtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16710.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
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--------------------------------------------------tgacttctctcctgtaattgagaatagaccactgactt--ttgccgtcatgaaggaaattattctcatcacttttaaattct---atttattccttatttgt-----tagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 7
gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
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----------------------------------------------------------agcatatgacactaatattctcaacaaaatattgtattccttattttcttatctacaaatagat-attccttatttactcctaattttcccacca-tgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 8
gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
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--------------------------------------------atgattaaactcctaactg--gtttcctgcagagaaagaattccatttggtgcgt---------gtttatgctttggtta-----tatataaaacatttttaattgatgttaccagGTGCCTGGAGCTGAAGCTCTTGTTATAAGAGTTGTGTCATCTGTAGACAAGAAGTTAGAAGTTAAACAGAGGTTTTTGGAGATTTTTCAGGAAGAAAATT
upper sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 10
gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagt---gctacttcactggaaac-aatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
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-----------------------------------------------------------ttttttaatgtttcttggatattgattattacactcgttgctagcatatcctggttttcta-tggattactaatttcata----ttcacttggatgtgttgccagATTCCTGGGGCTGATGCTCTTGTTGTAAGAGTTGTGTCATCTGTTGACAAAAAGTTAGAAGTGAAACCGCGGTTTCTGGAGATTTTTCAGGAAGAGAATTMapped 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|116434362|gb|EG476954.1|EG476954EST: AGCAGGAAAGGACTGAGAGAGCCAGGGTTCAAGGAACAAGTTATGATGAG ATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGGACTGAGAGAGCCAGGGTTCAAGGAACAAGTTATGATGAGgtaatctggc ... gcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
tgattgtttaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctggcggtggaatacagggttttaaagtctcatgtgattttgcattgagtcctatcttctattgtttgttgaagtgctacttcactggaaacaatagattgaagcttactggttggtcactgattgtttaatttttcttttactggcactaacagATTCCAACTGTTGAATCCCTTGTGGTTAGAGTTGTTTCATCTGTTGACAAGAAGCTAGAAGTTAAATCTCGATTTCTTGAAATTTTTCGGGAGGATAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT