Sequence
atgc intronic sequence ATGC exonic sequencegtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatccagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttggattcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G75850.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 17
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatccagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcatt-ctcaatattttgtcttatcttggattcatga-acagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
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-------------------------------------------------------------------------------------------------gtattgctgtaacaa--ttgatttatgctttccataactctgcatatcatgtaa-ctacctttcatattacagGCGGCCAATGATTGTGATCTGGAACCGGTTGCTTATGAGTTCTTTACTCAAGCATTCATCTTATATGAAGAAGAAATTGCG
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 17
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatccagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttggattcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
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-------------------------------------------------------------------------------------------------gtatgcttgtaatactgcatatttttgtaagtcttcctct---tattatctgattatgtttcttgatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATATTATATGAAGAAGAAATTGCG
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 17
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatc-cagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttggat-tcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
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----------------------------------------------------------tttcctgacattgtagagactctttatcctgattattacaaatctctcatttcacaactgtttcag------------taattttttttctcacttttattattaatatcagGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGCG
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 18
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatccagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttggattcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
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--------------------------------------------------ttcctgacattgttgagactctttatcttgattatgacaa-atctctgatttttcaca-------agtgttt----cagtgattttttttctcacttttattattaat-----atcaGGCTGCTAATGACTGTGACCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTTGTATTATATGAAGAAGAAATTGC-
upper sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 17
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatccagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttgg--attcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
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--------------------------------------------------------------------cactgaacagagtctttaatattgttactgactaggtgttggtgggcaagaattgt--ttgtttctctaacctgtatttataccttgatcattgataaccagGCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCGMapped 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|125072549|gb|EL137199.1|EL137199EST: CAGTTCCATGTCCTGAACTGGCTCTAAGGCTCTACCTTCAGTGCGCAGAG GCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTT
genomic: CAGTTCCATGTCCTGAACTGGCTCTAAGGCTCTACCTTCAGTGCGCAGAGgtaatttata ... tcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagaatctgacatagcattctcaatattttgtcttatcttggattcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
atctgac putative branch site (score: 3)
aatattttgtcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttatagggttagggttactattatttcgaactcagaataacgtgacttacaatattaatggaatccagtaatctattgttcattttatctcagtttttttgtagcaaggcagaatctgacatagcattctcaatattttgtcttatcttggattcatgaacagGCCGCAAGTGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTTACCCAAGCATTTATGTTATACGAGGAAGAAATTGCG
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