Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgtgcatctatgttgcaaggttggtcacatatttagttagatgaatgcttaaagtaatccttgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12370.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 5
-----gtaagtgtgcatctatgttgcaagg--ttggtcacatatttagtta-gatgaatg--cttaaagtaatcct--tgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
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gtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 5
---gtaagtgtgcatctatgttgcaaggttggtcacatatttagttagatgaatgcttaaagtaatccttgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
|| || | | || | | || | | | | || | | | | || ||| | || | |||||||| ||||||| ||||| |||| ||||| || || ||||||||||| || | ||||||||||||||||| || |||||||||||||| || || ||||
gtaataccagttcgttcatttggttt--ttaattttaccatcatttgtgttaggaaatttacctatggttgattaatatctgcagTACTTAATGGAATTCAATAGCAGTCCAGGCGACCTGATGGAGCTTTCACCTCTTTTTTCTGATGATAGCCGTGTTGCTGAGGCTGCTTCGATTGCCCAGA
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 5
---gtaagtgtgcatctatgttgcaaggttggtcacatatttagttagatgaatgcttaaagtaatccttgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
|| || | || || || | | | | || | | | | || || | || |||||||| ||||||| ||||| |||||||||| || || ||||||||||| || | ||||||||||||||||| || ||||| |||||||| || || ||||
gtaataccagtttgttcattttttttttttaattttaccatcatttgtgttaggaaatttacctatggttaattaatttctgcagTACTTAATGGAATTCAATAGCAGCCCAGGCGACCTGATGGAGCTTTCACCTCTTTTTTCTGATGATAGCCGTGTTGCTGATGCTGCTTCGATTGCCCAGA
upper sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgtgcatctatgt-tgcaaggttggtcacatatttagttagatgaatgcttaaagtaatccttgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
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gtat-tatctatcaagacacataaaattgattaccatttgcatagaatgagttaatatcactttgttgatttcatctctgcagTACTTGATGGAGTTCAATAGCAGCCCAGGCGACCTGATGGAACTTTCACCTCTATTTTCTGATGATAGTCGTGTTGCTGAGGCTGCTTCAATCGCACAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcacatatttagttagatgaatgcttaaagtaatccttgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
atatttagttagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgtgcatctatgttgcaaggttggtcacatatttagttagatgaatgcttaaagtaatccttgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT