Sequence
atgc intronic sequence ATGC exonic sequencegtataacacaaaatttacaatttcccttgggtggtttaattagaattttggtgttgaattggttttgtggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G35690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G04940.1 (Glycine max), 3'ss of exon 3
------------------------------------gtataacacaaaatttacaa---tttcccttgggtggtttaattagaattttggtgttgaattggttttgtggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
| | | | | | || || | | ||| || | | | | ||| | | || | || ||||||||||||| ||||| || ||||||||||| || ||| |||| || | ||||||||| |||| ||| ||||||||| |||||||| |||||||| |
gtacaattcagttaattgtcctgatggcattcttttctttgatatattacctaaaaagatatatattgatgaaaatactcatgagataggtctagctcataaattcttttg--cagGGAATGTTTGTTCCTGCTATCAAAGGACAAGGAACTGAGGAACAGCAGAAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGTTATGCCC
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G15320.1 (Glycine max), 3'ss of exon 3
------------------------------------gtataacacaaaatttacaatttcccttgggtggtttaattagaattttggt--gttgaattggttttgtggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
| | | | | | || || | | | | | || || | | | || | | | | | ||||||||||||| ||| | || ||||||||||| || ||| |||| || || ||||||||| |||| ||| ||||||||| |||||||| || ||||| |
gtacaattcagtcaattgtcctgatggcattcttttctttgatatactacctataaatatatatatg-gatgaaaatactgatgagataggtctagctcataaattattttgcagGGAATGTTTGTTCCTACTATCAAAGGACAAGGAACTGAGGAACAGCAGCAGAAGTGGTTGCCTTTGGCTCATAAGATGCAAATAATTGGTTGCTATGCCC
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 3
------------------------gtataacacaaaatttacaatttcccttgggtggt-ttaattagaattttggtgttgaattggttttgtggtgg-atagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
| | ||| || | || |||||| | || || | | | || | ||| || | | | ||||||||||||||||||| || ||||||||||||| || |||| || || ||||||||| || ||||| || |||||| |||||||| || ||||| |
atataatattgagcgggtgttttcactttccgtggaatatatatatt---ttgggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 2
----------------------gtataacacaaaatttacaatttcccttgggtggtttaattagaattttggtgttgaattggttttgtggtgg-atagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
| || ||| || | | |||| | || || | | | || | ||| || | | | ||||||||||||||||||| || ||||||||||||| || |||| || || ||||||||| || ||||| || |||||| |||||||| || ||||| |
ataatattgacagggtgttttcactttccatggaatatatatatatttttggtagcattgctttgtgtactaaattttagttgtttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATTGGTTGCTATGCCC
upper sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 3
-------------gtataa-cacaaaatttacaatttccctt-------gggtggt-ttaattagaattttggtgttgaattggttttgtggtgg-atagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
|||| ||| ||| || | || |||| | || || | | | || | || || | | | ||||||||||||||||||| || ||||||||||||| || |||| || || ||||||||| || ||||| || |||||| ||||| || || ||||| |
gaatattgtccaggtattttcactttctttggtatatatttttgggagggggtagcattgctttgtgtactaaattttagttatttatattcttttgcagGGAATGTTTGTGCCTGCTATCCAAGGACAAGGCACTGACGAACAGCAGCAGAAGTGGTTGCCTCTAGCTTATAGGATGCAAATAATCGGTTGCTATGCCCMapped 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|116443143|gb|EG485735.1|EG485735EST: TCAAATTGAGATCTTTCATGGATCAACCAGGCTTCTTGGATCTGCATTGG GGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAA
genomic: TCAAATTGAGATCTTTCATGGATCAACCAGGCTTCTTGGATCTGCATTGGgtataacaca ... tggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAA
EST:
gi|116443141|gb|EG485733.1|EG485733EST: TCAAATTGAGATCTTTCATGGATCAACCAGGCTTCTTGGATCTGCATTGG GGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAA
genomic: TCAAATTGAGATCTTTCATGGATCAACCAGGCTTCTTGGATCTGCATTGGgtataacaca ... tggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccttgggtggtttaattagaattttggtgttgaattggttttgtggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
gtttaat putative branch site (score: 4)
tttaattagaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataacacaaaatttacaatttcccttgggtggtttaattagaattttggtgttgaattggttttgtggtggatagGGAATGTTTGTGCCTGCAATTAAAGGACAAGGCACAGAGCAACAACAACAAAAGTGGTTGTCTTTAGCTACTAAGATGCAGATAATTGGATGTTATGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT