Sequence
atgc intronic sequence ATGC exonic sequenceTGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatatttacataccaaagttttccgtttgggtcccctcttgcattcttcagtcatctctatctcaattactctttaatgtatctctgattcaatgctttaatattgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23880.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G075260_T02 (Zea mays), 5'ss of exon 5
TGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatatttacataccaaagttttccgtttgggtcccctcttgcattcttcagtcatctctatctcaattactctttaatgtatctctgattcaatgctttaatattgcag
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TGCTCCCTTCTGGTGATTGACAGAGGAAACCAAGCAATTAGAGAGATTCAGCTCCACTTTGATGACTGTGTGTACCAGTATGAAGCTGGTTTTCCTCTAGgta-tatt-atacactgctcctttcctatcgtagcaggcctggcatagtggtgaga---ctgtcttactgagtcaccaa---gttgcgggttcgaagc---aacctctccg
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G125455_T03 (Zea mays), 5'ss of exon 5
TGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatatttacata--ccaaagttttccgtttgggtc------ccctcttgcattcttcagtcatct-ctatctcaat-tactctttaa--tgtatc-tctgattcaatgctttaatattgcag--------
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TGCTCGCTTCTGGTGATTGACAGAGGAAACCAAGCAATCCGGGAGATTCAGCTCCACTTTGATGACTGTGTATACCAGTATGAAGCTGGTTTTCCTCTAGgtatattatacattgctcaaatttttctgcaatcatcgcaggacctgaaaacatatgactgaaacttaccacctaaacatgcagtttaaactctataatacaactgatcatattaactttccatgcctgcag
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G39910.1 (Glycine max), 5'ss of exon 6
TGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatatttacataccaaagttttccgtttgggtcccctcttgcattctt--cagtcatctctatctcaattactctttaatgtatctctgattcaatgctttaatattgcag
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TGTTCGCTACTCGTCATAGACAGAGGAAACCGAGCCATCAGGGAGATCCAACTCCATTTTGATGATTGTGCTTATCAATATGGCAGTGGATTCCCACTTGgtaaactaaatcatacatgattttctgtagaaattctgtcaagtgttattgttaatcaaatttagactgattgc-cttcaatgttacag------------------------
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G18550.1 (Glycine max), 5'ss of exon 4
TGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatattta-cataccaaagttttccgtttgggtcccctcttgcattctt--cagtcatctctatctcaattactctttaatgtatctctgattcaatgctttaatattgcag
||||| | || ||||| ||| ||||||||| |||||| || ||||| |||||||||||||| || ||||| |||||||||| ||||| || || || ||||| | | ||||||| |||| || | | || | || || | ||| | || ||| | ||| ||||| |
TGTTCACTACTCGTCATAGACAGAGGAAACCGAGCCATTAGGGAGATCCAACTCCATTTTGATGATTGTGCCTATCAGTATGGCAGTGGATTCCCACTTGgtaaactaaatcataccatgaatttctgtagaaattctgtcaagtgttattgataatcaaatttagactgattgc-cttcaatgttacag------------------------
upper sequence: AT1G23880.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0026g00330.t01 (Vitis vinifera), 5'ss of exon 5
TGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatatttacataccaaagttttccgtttgggtcccctcttgcattcttcagtcatctctatctcaattactctttaatgtatctctgattcaatgctttaatattgcag
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TGCTCCCTACTTGTCATAGACAGAGGAAACCAGGCAATTCGGGAGATCCAACTTCATTTTGATGACTGTGCTTATCAATATGGAAGTGGTTTCCCTCTAGgtaa-actgatccatccagtattgatctttgatacttctc----aatcttga--caaatccatgtgaaatgttctcca-tg-attgcag----------------------Mapped 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|125211422|gb|EL226376.1|EL226376EST: GTGCTGATCAGTATGGAAGTGGCTTTCCTCTGG GGATTGCAGTTCTTGTAGCGGCAGTTTTCTTTGGCTATATGCTGGCCTTGT
genomic: GTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatattta ... aatattgcagGGATTGCAGTTCTTGTAGCGGCAGTTTTCTTTGGCTATATGCTGGCCTTGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTTCCTTGCTAGTCATTGACCGAGGAAACCAAGCCATCAGAGAGATTCAACTCCATTTTGACGACTGTGCTGATCAGTATGGAAGTGGCTTTCCTCTGGgtaatatttacataccaaagttttccgtttgggtcccctcttgcattcttcagtcatctctatctcaattactctttaatgtatctctgattcaatgctttaatattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG