Sequence
atgc intronic sequence ATGC exonic sequencegtaacaattctttcaatctaattttaactgctgtcataaccttcgcttatttctgtaaaagttcagtatctaactcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11980.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 8
gtaacaattctttcaatctaattttaactgctgtcataaccttcgcttatttctgtaaaagttcagtatctaactcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
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gtaattagcattttcttgtaaattttattagagt----attcacgctgcaaacagaacctattct-tattgatgatgttatctgcatgcagAGCTGTGTTAAATTTGTTTTCAAAGAACATGGGTACAGCAGTCGAGAATTTTCAG
upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G006781_T01 (Zea mays), 3'ss of exon 8
gtaacaattctttcaatctaattttaactgctgtcataaccttcgcttatttctgtaaaagttcagtatctaac----tcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
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------------gtaattggtgtttaaattatagaattttattag--tgactctaaaggggttttattattgatgctgccatctgcattttgcagTGCGGTTCTAAATTTATTCTCAAAGAATATGAGTACGGCGGTCGAAAATTTTCAG
upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: AC235544.1_FGT004 (Zea mays), 3'ss of exon 8
gtaacaattctttcaatctaattttaactgctgtca-taaccttcgcttatttctgtaaaagttcagtatctaactcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
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gtaattggtgtttaaat----tattgaattttatcactgactctaaaggggctttgtta---ttgatgctgttatctgcatttt----gcagCGCGGTTCTAAATTTATTCTCAAAGAATATGAGTATGGCGGTTGAAAATTTTCAG
upper sequence: AT5G11980.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G22880.1 (Glycine max), 3'ss of exon 7
gtaacaattctttcaatctaattttaactgctgtcataaccttcgcttatttctgtaaaagttcagtatctaactcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
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gtaaaacatgctccttttca---tgatctattaggataaattgtacttaaagcattt----tctaatatataagatgttttctt--tacagAGCTGTTCTCAACTTATTCTCCAAAAATATGAGTACTGCAGTAGAGAATTTTCAGMapped 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|124732117|gb|EH823519.1|EH823519EST: GGTGGGGTTGGGCTAGACTTCCGGGGTCTGCTTCCTCCACTTTTTGAAGA GGCGGTTCTAAACTTATTCTCC
genomic: GGTGGGGTTGGGCTAGACTTCCGGGGTCTGCTTCCTCCACTTTTTGAAGAgtaacaattc ... cttactacagGGCGGTTCTAAACTTATTCTCC
EST:
gi|116461241|gb|EG503833.1|EG503833EST: GGTGGGGTTGGGCTAGACTTCCGGGGTCTGCTTCCTCCACTTTTTGAAGA GGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTT
genomic: GGTGGGGTTGGGCTAGACTTCCGGGGTCTGCTTCCTCCACTTTTTGAAGAgtaacaattc ... cttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaccttcgcttatttctgtaaaagttcagtatctaactcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
tacttac putative branch site (score: 1)
ttatttctgtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaattctttcaatctaattttaactgctgtcataaccttcgcttatttctgtaaaagttcagtatctaactcgcatacttactacagGGCGGTTCTAAACTTATTCTCCAAGAACATGAGTACAGCAGTTGAGAATTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC