Sequence
atgc intronic sequence ATGC exonic sequenceTTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.4 |
intron # | 20 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 20
TTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcattactgtt-cacttggccgtttggaaaaat-----caaatatgtgtctttt--------gttatctttatgac-aagaaattatcttgacag
||||| |||||||||||| || ||||| ||||||||||| || ||||||||||||| | |||||| ||| ||||| || || || | ||||| || ||||| | || ||| || || ||| | | | | | | | || |||| ||||| | || || |||
TTGCAATCCTTGCTAAGGAGCAAGGGAAAAACAATGTTGCATTCCTTTGCTTATTTATGTTGGGTAAATTAGAAGACTGCCTTCAACTGTTGGTAGAAAGgtaatcttctaaagttgtgctcttccctttatgacattactgatagggaaggattgattagaatgcagttacatttatagttgaagtatgccttttgcag
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 20
TTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcattactgttcacttgg---ccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaag-aaattatcttgacag--------------------
||||| |||||| ||||| || ||||| ||||||||||| || ||||||||||||| | |||||| ||| ||||| || || || | ||||| || ||||| || || ||| || || | || | | ||| | || ||| | | | | | ||| || | ||
TTGCAATCCTTGCCAAGGAGCAAGGGAAAAACAATGTTGCATTCCTTTGCTTATTTATGTTGGGTAAATTAGAAGACTGCCTTCAACTGTTGGTAGAAAGgtaattttctaaagttgggctgttttccttcctgacattactgatagggaggattgattagaaatttagaatgcagtttacatttatagctgaagtatgccttttgcag
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 20
TTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtattt-----cattactgttcacttggccgtttggaaaaat-caaatatgtgtcttttgttatctttatgacaagaaattatcttgacag
|||||| ||||||||| ||||||||||||||||| |||||||| ||||| || || | | |||||| ||||||||| ||||||||| | |||||||| ||||| || |||||| || ||| || | | | || | || | || | || | ||| |||| |||
TTGCATCCCTTGCTAAAGAACAGGGGAAGAACAACGTTGCCTTCCTTTGTTTGTTCATGTTGGGTAAATTGGAAGAGTGTCTGCAGCTGTTGGTGGACAGgtaattgttgttgttactgcaaacatgggaacaaagatagttgtggagatat-tccacttttgggatgatactgaagcattctctttgcag
upper sequence: AT3G15980.3 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 20
TTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgta-----tttcattactgttcacttg------gccgtttggaaaaatcaaata--tgtgtcttttgttatctttatgacaagaaattatcttgacag---------------------------------------------------------------
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TTGTTTCACTGGCTAAAAAGCAGGGGAAGAATAATGTCGCATTCCTTTGTTTATTCACGCTGGGTAAATTGGAAGAGTGCCTTCAGCTGTTGGTGGAGAGgtaatcattttccttaccatataaccatagaaaatcaactgctgatactaatttattacacatttacttatttcatttaacagacaatatggtggtagtttatatgacccaggaagttgagattgagtttactgattagactctgatatggtctgttgcagMapped 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|125289748|gb|EL303833.1|EL303833EST: TTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAG TAACCGGATACCAGAAGCTGCT
genomic: TTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcatt ... atcttgacagTAACCGGATACCAGAAGCTGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGCATGCCTTGCTAAGGAACAGGGGAAGAACAATGTTGCCTTTCTTTGCTTATTTACGCTGGGTAGATTGGAAGATTGTCTGCAGTTATTGGTGGAGAGgtatttcattactgttcacttggccgtttggaaaaatcaaatatgtgtcttttgttatctttatgacaagaaattatcttgacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA