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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgttactaatcatcagcatctctggttttttttgtgtgaatcttatattggtttattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA

Basic information

species Arabidopsis thaliana
transcript AT4G01370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 2
-------------------------------gtacgtgttactaatcatcagcatctctggttttttttgtgtg-aatcttatattggtttattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA
                                 | |  |   || | |  || | |  |  ||||| |    ||  |    || | |   | ||   ||||| ||  |  ||||||| || |||   |||||   ||| ||||||||||||||||| |||||||| |||||||| |||||||||||||| |||||  || 
gtcttttatcttggcaatactagggattgttagatgattagatagtaacaagaaacaattttttttgtgacttgtgacaaaatctagccatttttcacagGTCATCTCAATAAAGGACATCATACGGCCACCAAGGAGGGAGAACTTCAATGATGTCTACATTGTCTATGAGCTCATGGACACTGATCTTCACCACCTTC

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
---------------------------gtacgtgttactaatcatcagcatctctggttttttttgtgtgaatcttatattggttt----attg---tgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA
                           |  ||||| |   ||  |   | || |   ||| | |  | | | ||| ||  || |||    | ||     ||| | |||||  ||||||| |||||    || ||    ||||| ||||| ||||||||||||||||||| |||| | ||||| ||||||||||| || || |
ttccttttttttttgttgggcggtcaagagcgtgtgatacatttttgac-tcacacatttatatcatat-agtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
-------------------------gtacgtgttacta--atcatcagcatctctggttttttttgtgtgaatcttatattggtttatt-----gtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA-
                          |   |  ||| |  || || || || ||   ||        |    ||   ||    ||  ||      |||||||||| ||  | || || || |||  |||||| ||||| || |||||||||||||| ||||||||||||||| | ||||| |||||||| || ||||| | 
tttcatgggagcttcctgattggattttaattctacaatcattattagaat-tcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 2
----------------------------gtacgtgttactaatcatcagcatctctggttttttttgtgtgaatcttatattggtttatt-----gtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA
                              |  |   | | || || || || ||   ||        |    ||   ||    ||  ||      |||||||||| ||  | || || || ||   |||||| || ||  | ||||||||||| || ||||||||||||||| | ||||| |||||||| || ||||| |
gtttcatgggagtttttttattggattttaattttacattcattattagaat-tcaatttgaaacaaggctgctcacttaccaattacttctctaatgcagGTGATAGCCCTTAAAGACATTATTCGACCACCACAAAGGTATAACTTCAATGACGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAA

upper sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtacgtgttactaatcatc-agcatctctggttttttttgtgt--gaatcttatattggtt-----------tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA
                  ||  ||   | | |   || || || | |  | ||  |  ||   ||||  ||||||   |           |  |  |||||| ||||   | || || || |||   |||||  |||| ||||||||||||||||| ||||||||||||||  | |||||||||||||| || || || |
ctttagttactttggttcgtttgttggattcaggttctagaattttttatgttcctcctggtggaataatatatttactatcagttcttatcctccgcagGTTATTGTCTTGAAAGACATCATACGGCCACCTAAGAGGGAGAACTTCAATGATGTCTACATTGTTTATGAATTAATGGACACTGATCTGCATCAGATAA

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|86026209|gb|DR321962.1|DR321962
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAA
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAA
EST: gi|86026213|gb|DR321966.1|DR321966
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026222|gb|DR321975.1|DR321975
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026210|gb|DR321963.1|DR321963
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026217|gb|DR321970.1|DR321970
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026226|gb|DR321979.1|DR321979
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|116416232|gb|EG458824.1|EG458824
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026211|gb|DR321964.1|DR321964
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAA-GGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026216|gb|DR321969.1|DR321969
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAC-G-ATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026224|gb|DR321977.1|DR321977
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026229|gb|DR321982.1|DR321982
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026214|gb|DR321967.1|DR321967
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATA
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATA
EST: gi|86026208|gb|DR321961.1|DR321961
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCATAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026227|gb|DR321980.1|DR321980
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026207|gb|DR321960.1|DR321960
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026228|gb|DR321981.1|DR321981
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026215|gb|DR321968.1|DR321968
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026230|gb|DR321983.1|DR321983
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026212|gb|DR321965.1|DR321965
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026218|gb|DR321971.1|DR321971
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|86026206|gb|DR321959.1|DR321959
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
EST: gi|116451512|gb|EG494104.1|EG494104
EST:     AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAAT                         GTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT
genomic: AAAGGACTTTGAGAGAGATTAAGCTTCTCAAGCATATGGATCATGAAAATgtacgtgtta ... tattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcagcatctctggttttttttgtgtgaatcttatattggtttattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA
 tactaat  putative branch site (score: 1)
                                  ttatattggtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgttactaatcatcagcatctctggttttttttgtgtgaatcttatattggtttattgtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT