Sequence
atgc intronic sequence ATGC exonic sequencegtgagcaggtatctttttcttatgacttatgagtatttgtaaagtttgtaatatgaatagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G64560.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 5
-----------gtgagca-ggtatctttttcttatgacttatgagtatttgtaaagtttgtaatatgaatagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA
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tctattctcttgcatacttggtgtgtatcacccgttatttactagcttttcttgttcatgctttcctattagatcacaaaatg--tttgttctctttgccagGTGAGAGATGAACTTGAACAATTATTGGACGATGACGATGACATGGCTGATCTTTACTTGTCCAGAAAGTTGGCTGGGGCAGCTTCCCCTGTCAGTGGCT
upper sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G32350.1 (Glycine max), 3'ss of exon 5
-------gtgagcaggtatctttttcttatgacttatgagtatttg-taaagtttgtaatatgaa--tagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA---
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tagtttaatgtgactgtaaactgccttgatcagttttaagtagaaaacaacatatatcctttgtccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTATACCTGTCAAGAAAGGCT---GGTTCAGCATCACCAGTTAGTGGATCAG
upper sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G35260.2 (Glycine max), 3'ss of exon 5
-------gtgagcaggtatctttttcttatgacttatgagtatttgtaaa---gtttgtaatatgaatagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA---
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aagtttaatgtgaatgtaaactgccttgatcagttttaaatagaaaacaacatatatccattttccctctcccatcacaagttcttgttatctggtacagGTCAGAGATGAGCTTGAACAATTGCTGGATGATGATGATGATATGGCTGACCTGTACCTGTCAAGAAAGGCT---GGTTCAGCATCACCAGTTAGTGGATCAG
upper sequence: AT5G64560.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 5
---------gtgagcaggtatctttttcttatgacttatgagtatttgtaaagtttgtaatatgaata--gagaact--aagtagc-ttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA
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acattttccatcagcagcagttgatcaattat--ctgctca--atttgtatgcttcacagccttaacactaaagacttcatatggtgctcataactgattgcagGTGAGGGATGAGCTTGAACAACTTCTGGATGATGATGATGATATGGCTGATCTTTATCTGTCCAGAAAATTGGCTGGTGCATCTTCACCAGTTAGCGGCTMapped 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|164215659|gb|ES110040.1|ES110040EST: TTCGGAAATTGAAGAGTGCCATGACTCGGTTGACAGCTCGGGTTCAAAAG GTAAGAGATGAACTCGAACAGTTGCTGGATGA
genomic: TTCGGAAATTGAAGAGTGCCATGACTCGGTTGACAGCTCGGGTTCAAAAGgtgagcaggt ... ccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtaaagtttgtaatatgaatagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA
cttcatcgcctttt CT-rich tract
tttgtaatatgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcaggtatctttttcttatgacttatgagtatttgtaaagtttgtaatatgaatagagaactaagtagcttcatcgccttttgcagGTAAGAGATGAACTCGAACAGTTGCTGGATGATGACGATGATATGGCAGATCTTTACCTTTCAAGGAAACTTTCAAGTGCTTCCTCACCGATTAGTAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA