Sequence
atgc intronic sequence ATGC exonic sequence...tcgagcaaatgggcgatagctatattttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16155.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 5
tcgagcaaatgggcgatagctat--attttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
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catgttaaattctaattaaccatctatgctgttttatgattaaggcctgttgtcatctgatgatatttc--acctgtatttacctaaatttcacttggacagGTTACTTTTGTTGAAGCACTTGATCAGTTGATGCCTGGTTTTGATCCTGAGATTGCAAAATTGGCCCAAAGGATTCTTATCAATCCTCGTAAAATTGACT
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 5
---tcgagcaaatgggcgatagctatattttgctt--aaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
| || | | ||| || ||| || || ||| |||| | ||| ||| || | || | || || | || | ||||| |||||||| || || | |||||||| |||||||||||||||||||| || || ||| ||||||| ||||| || |||||| | | || |||||||
agtccaagaagttaaaaaatatttaatctttattttaaaaatttatgatccctaatttatccctgaaaagataag---caaagtaataattggtattct--gcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------------------tcgagcaaatgggcgatagctatattttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
| | || | | |||||| | || | ||||| | | | | || | || | | | | | | | ||||| ||||||||||| || | || || || |||||||||||||||||||| || || ||| ||||||| |||||||| |||||| | | || |||||||
gtagtacttctcttctgatatatttttttttatcctttctcaattgtattttgttcatgagaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattat-ctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcagGTTACTTTTATTGAAGCTTTAGACCAGCTCATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTTCTCATAAATCCCCGGAATATTGACT
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 5
----tcgagcaaatgggcgatagc-tatattttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
| | | | || | | | |||| || || |||| | | | ||| || | || || || | || | ||||| |||||||| || || | |||||||| |||||||||||||||||||| || || ||| ||||||| ||||| || |||||| | | || |||||||
aatatttaatctttatactatttcctttttttttaaaaaaaattatgatccctaatttattcctgaaaagattag---caaattaataattggtattct--gcagGTTACTTTTATAGAAGCTTTAGATCAACTTATGCCTGGATTTGATCCTGAAATTAGCAAGTTGGCTCAGAGGGTCCTTATAAATCCCCGGAATATTGACT
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ06739 (Selaginella moellendorffii), 3'ss of exon 5
tcgagcaaatgggcgatagctatattttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
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--------------------------------------------gtttagtttttctt----ctttcctttttctatagaatacgcga-----tgtgcagGTGACTTTTGTTGAAGCTCTGGATCAACTGATGCCAGGCTTTGATCCTGAAATCGGGAAGCTTGCTCAGAGGCTCCTGATCAACCCTCGAAAAATTGATTMapped 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|125047642|gb|EL119911.1|EL119911EST: TTATATCGGTCTTGAGTTCAGTGTATGTTTACACGGCCCTTGGAAGTGAG GTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTG
genomic: TTATATCGGTCTTGAGTTCAGTG-ATGTTTACACGGCCCTTGGAAGTGAGgtaacatttt ... ttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTG
EST:
gi|124873042|gb|EH954687.1|EH954687EST: CCCTTGGAAGTGAG GTAACTTTTACTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAG
genomic: CCCTTGGAAGTGAGgtaacatttt ... ttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
ctctttttttttttta CT-rich tract
aactcttttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgagcaaatgggcgatagctatattttgcttaaggtttgtgatgctctgcaactccaggaagtgaccaagctcaggggaactcttttttttttttacagGTAACTTTTATTGAGGCACTGGATCAACTAATGCCTGGATTTGATCCTGAGATCAGTAAGCTGGCTCAAAGGGTTCTAATAAATACAAGAAAAATTGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- gagcaaa
- - - - - - - - - - - - - - - - - ggtttgt
- - - - - - - - - - - - - - - - - - - - - atgctct
- - - - - - - - - - - - - - - - - - - - - - - - - -aactcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accaagc