Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27600.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
-------------------------------------gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttct--ttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
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gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagta-attcctcactgttattgtttttgtacatta-tcacttctcacactcttccataacgcaaattctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG
upper sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
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-ttaaccccaaataagtctaggtttcatcttca-actaaaatattgtttttt---tttgcgtgctatcac--actctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG
upper sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
--gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
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aatcaaatgacatccatatccaaaataattgggtgtgcc----tttgtgcttttgtattattgtcacagtttcgtaatgtggatctt-----tgtgtttccattttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG
upper sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 16
gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
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-taattgccggatgtctttaagaaaatggtattca-caactaatgaactaattca-ctgagttgtgtggattctggttgctccctg----cccttttcctctttcagAAATAAAGCTTGTGGATGTTCCTGAAATGAATTACACCTCTGAGGATCAGCCCTATCCTCGCGGTGAAATATGTGTCAGGGGTCCCGTTCTCTTCCAAGGMapped 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|164073483|gb|ES077704.1|ES077704EST: TGGTGACAATTTATCTGGCCATGTCGGTTCCCCTAATCCAGCTTGCG AGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAAC
genomic: TGGTGACAATTTATCTGGCCATGTCGGTTCCCCTAATCCAGCTTGCGgtaagcaatg ... tctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
tgttttttctttctt CT-rich tract
ttttgaaaatgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaatgtgttattttaaagacagtgtatatatcagaatccaaacttttgtatccaaattgtatgactggtttttgtgttttgaaaatgttttttctttcttagAGGTAAAACTTGTGGATGTTCCCGAAATGAATTACACATCAGACGATCAACCATACCCACGTGGTGAAATCTGTGTAAGAGGACCAATCATCTTCAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA