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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA

Basic information

species Arabidopsis thaliana
transcript AT2G44610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 2
gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
||| |||        |   |  |||| |   || |         | |||   |||         |   | |        |      |  |    ||||||||||||||| || || |||||||||||| | ||||| ||||||||||| || || ||||||||||| || || | |||||||||||
gtatgatggcatcttttgctgcatttccagttagttgttctactccttgggaatcggcaggcattatcttatgcattttgtatttttttttctgcagGGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G075719_T01 (Zea mays), 3'ss of exon 2
gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
|||  ||    |  ||  | ||    |      ||| |      |||||      |      | |||       |  | |  |   || |    ||||||||||||||| || ||  | ||||||||| ||||||| ||||||||||| || || || |||||||| ||||| |  ||||||||||
gtataattacta--ctactgcatccgttagc--ctgtatggccccattgtgatctacggaccgttgaccttatgcatgtgttgttttcttt--gcagGGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 2
gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatc--gagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
      | | | | ||  | |    |||  |  |||     |  |  |  |||||   | | ||   || || |   |   |    | |    |  ||||||||| ||||| || ||  ||||||||||| ||||||| |||||||| || || || || |||||||| ||||| |  ||||||||||
-----gtatggtgactactactgcattcatagcctgtt---tgccccttgagatc---tatggactgttgaccttatgcatgttttattttctttgcagGGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 2
gtaagatcttgagcctct-ttcaattttcgaatactgaagaataacattgcaga-tcattttttgatgattaacatcgagagccg-aaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
||      ||| |  |   |||||||   ||   |     | |    | |  || |  ||||||      ||| ||  |       |  |  ||||||||||||||||||||||| ||  |||| || ||||| ||||| ||||| |||||||| || || || ||||||||||| |||||||||||||
gtgcatcgttgggttttggttcaattaatgacacccctttatttgactggtggagtttttttttcccccctaatattcatcttttcatgtgttatgacagGGATACAGCTGGGCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATCAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G05860.1 (Glycine max), 3'ss of exon 2
----gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcat--atgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
    | |  |   |    || |||   ||||    || ||||   |   | |     |||| |    |   || || |  |         ||||   |||||||||||||||||| || ||  |||| || ||||| ||||| ||||| || ||||| || || |||||||| ||||| |||||||||||||
ataagcagtacactatagctttttttttttttt--tattgaattctcttagttttcttcatctcaacacc-ttcacttttaatttttttttcatttgtgacagGGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G16200.1 (Glycine max), 3'ss of exon 2
--gtaagatcttga-gcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
  | |  |   ||  | || |||   |||     || ||||   |   | |     || | |    |   |||   |  |            | |||||||||||||||||| || ||  |||| || ||||| ||||| ||||| || ||||| || || |||||||| ||||| |||||||||||||
aagcagtacactgttggctttttatttttatttttattgaattctcttaattttcttcctctcaaaacctttactttttatttttcttcatttgtgacagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 2
gtaagatcttgagcctctt--tcaattttcgaatactgaagaataacattgcagatcatttttt-gatgat--taacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
    | | ||    |  ||  | |     |   |  |||    |    ||     |  || |   | || |  |||  |  |       |    |  ||||||||||||||||| || ||  |||| || ||||| ||||| ||||| || ||||| || || || ||||||||||| |||||||||||||
--tgggttttagttcaattaatgacacaccttcttttgactggtggagttttttttttttctcccggtgttcctaatgttcatcttttcatgttttcgacagGGATACAGCTGGCCAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTAGCTGTTATTGTATATGATGTTGCAA

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S2_143V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------------------gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
                                                                                 |     | ||| |  |||| |      |  ||  |   |  |   |   || |||| ||  | ||  | | | |     || |  || |  |  |||||| |||||||| |||||||| ||||||||| | ||||| ||||| ||  |||| || ||||| || ||  |||||||||||       
gtaaagggcattgggacgtgcacgttaatatgcaattgagagcatttttgtcgttttgttctttgctgagcagtttaagttgctgtttgttgtgtttcttacgcgcccctcat-ttatcggttccgaaaacacatcaattgcttattgt-agcgtttgtggctgttatgacct--cagGGACACAGCTGGACAAGAGCGGTTCAGGAGTTTGATTCCTAGCTACATTCGGGACTCGTCCGTGGCAGTGGTTGTGTATGAT-------

upper sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagatcttg-agcctctttcaattttcgaatactgaagaataacattgcagatcattttttga-----tgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
 |  | ||||   |  |   || | | | | ||        ||| | | ||   ||   |||| |     | |||||  | ||  ||  ||||    | |||||||||| || || |||||  ||||| ||||||||||||| ||||||||| | ||||| || ||||| || || || ||||| ||  |||
-tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgc--aaatgtggttacagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA

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|164008413|gb|ES056055.1|ES056055
EST:     CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCT
genomic: CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCT
EST: gi|116467570|gb|EG510162.1|EG510162
EST:     CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
genomic: CTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
EST: gi|164055793|gb|ES099932.1|ES099932
EST:     TACCTTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAA
genomic: TACC-TTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAA
EST: gi|124916170|gb|EH990044.1|EH990044
EST:     CAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
genomic: CAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
EST: gi|125223275|gb|EL237360.1|EL237360
EST:     TCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG                         GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG
genomic: TCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTGgtaagatctt ... catatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA
                       gattaac  putative branch site (score: 2)
             attttttgatgattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcttgagcctctttcaattttcgaatactgaagaataacattgcagatcattttttgatgattaacatcgagagccgaaatcatatgacagGGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT