Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaacctaaacagatctctgaatgctcatactatgagaatactgttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 9
---gtaaaaaacctaaaca-gatctctga-atgctcatactatgagaatactgtta----tgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
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gtaatgtgcatctcaaccaagaggtgtaagatacttaaagtatgattacttttttttcactattgattgatatgcagtacttgtctgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAATTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG----------------------------
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 1
gtaaaaaac--ctaaac---agatctctgaatgctcatactatgagaa----tactgttatgttaattcgtctctctttgcttg-ctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
|||| | | || ||| || | || || | | ||||| | | |||| || | | | | |||| || |||||||| ||| |||| | ||||||||||| ||||| | || |||||||| |||||||||||||||||||||
gtaatatgcttctcaaccaaaggatttaagatacttaaagtatgattactttttctgtctctatacattgatacgtagtacttgtctgcagCTTAAATATAACGAAAGTGGGAAAGAAAAGAATTGTTTACCCCAAGTTGGCCAGTGGAATATGATGAACAAG----------------------------
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
----------------------gtaaaaaacctaaacagatct---ctgaatgctcatactatgagaatactgttat--gttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
||| | || | | ||||| || | || ||| || |||||| | ||| || |||||||| ||||| || | ||||||||||| | ||| | || ||||||||||||||||||||||||||||||
gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcactt--ctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG----------------------------
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 10
----------------gtaaaaaacctaaacagatct---ctgaatgctcatactatgagaatactgttat--gttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
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gtaatgtgcttctccttctaaagatctgatttgtcatatactgaaactttaatttaccttttccctgtcattcattaatttaaagcactt--ctgaatgcagCTTAAATATCACGAAAGTGGGAAAGAGAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG----------------------------
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaaaacctaaacagatctctgaatgctcatactatgagaa-tactg----ttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
|||| | | | | | | | || | |||| | || | || || || ||| | | || ||||| || ||||| || | ||||| ||||| |||||| | || ||||| |||||||||||||||||||||||
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA----------------------------
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 10
gtaaaaaacctaaacagatctctgaatgctcatactatgagaatactgttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
|| | ||| | |||| | || ||| | || || |||| | |||||||| || | || || ||||| || || || |||||||| |||||||||||||||||||||
-----------------------------gtatgtcttccgaagatcgttaattcaagc--tctaacgttttctg--acagTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG----------------------------
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 10
gtaaaaaacctaaacagatctctgaatgctcatactatgagaatactgttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
|| | ||| || |||| | || || | || || |||| | |||||||| || | || || ||||| || || || |||||||| |||||||||||||||||||||
-----------------------------gtatgtcttccgaagaccgttaattcaagc--tcaaacgttttctg--acagTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG----------------------------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|86072813|gb|DR368570.1|DR368570EST: TAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAGCTCCATGG CTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGT
genomic: TAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAGCTCCATGGgtaaaaaacc ... cttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctcatactatgagaatactgttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
tgttaat putative branch site (score: 3)
ttcgtctctctttgct CT-rich tract
ttatgttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaacctaaacagatctctgaatgctcatactatgagaatactgttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA