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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA

Basic information

species Arabidopsis thaliana
transcript AT4G03100.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
---------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
          | |  | ||   |    ||   | |   | |         ||        |||| ||  |||  || || |  |    |  ||||| |||||||  | || ||||| |||||||||||||||||||||||  | || |||||  | ||    ||||| ||    ||||| ||  |  |||  |
gtaatttttcttaccataagaatttttttacgtgatcaattgtatgctgatgcaagtgcgctaagatgagatagtt-cacttgca---ttcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
-------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagtt---actaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
        |     | ||||   |          |  |      |  ||| |    |    ||||||      ||     ||  ||   |  ||||| | |||||  | || || || ||||||||||||||||||||||||||||| || ||  | ||    || |||||    ||||| || ||  ||| | 
gtatttccttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
--------gtaaaaacaaagtta----acctttgttca---atgaataagaatcactgagtagttactaacatttgattcttgcat-tctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
        |   | || | | ||    ||  || ||||     |||  |  |   |||   | |        | | |||| |   |  |||       ||||| | |||||  |||| || || |||||||| ||||||||||||||||| || ||||| |||||||  ||||||||    ||||| |||||||  || |
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatctttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGAAACAGCAA

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
-----------gtaaaaacaaagt-taacctttgttca-atgaa---taagaatcactgagtagttactaacatttgattcttgcat-tctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
            | | |  |   | ||    || | || |||||   || | ||   |||  | |     |    | |||| |   | ||||       ||||| | |||||  |||| || || |||||||| ||||||||||||||||| || ||||| || ||||  ||||||||    ||||  ||| |||  || |
gccatattttgcttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaa-aatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACAAACAGCAA

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
------gtaaaaacaaagttaacctttgttc-aatgaataa---gaatcactgagt--agttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
       | ||| |      |    |||||  |   |||     |   ||  || |  | | | ||  | |   || |||  |  | | ||   ||||| | |||||||| || ||||| ||||||||||||||||||||||||||||| ||||| || |||||||| ||||||   |||||||||||||   |  
gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttcacc--agATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA-
                                                | |  |     ||  |  |  |    | | |  | | | || | |     ||||||  ||  | | |   ||| || ||| ||||| | || || || || ||||||||||| || |||||||||||||||||||| |||||  | || || | ||  || |    || |  || |   | || 
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctg--tttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGAT-ACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------------------------------------gtaaaaacaaagttaacct-ttgttcaatga-ataagaatcactgagtagttactaacatttgattcttgcattctctaac--tgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA-
                                                                                                           |    | ||| |    | |||||   ||   |  ||     |||  |    |     ||||||  ||  | | |||  |  || |||||   |||||  |||||||||| |||||||| |||||||||||||||||| | || ||| | ||   |   ||| |    | || |||||   |   |  
gtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcagATGGTTGATCCGCTAACGGCTCTGATGCATGCCGTTCAAGTGATGAACTTGTTGAAAACTTTGATTCTACGCACATTGAA-GGACCGGAAGGCTACTTTGC

upper sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------------------------------------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgat--tcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA-
                                                                                                             |   |||  || ||  |  |||| |  |  |   |||   ||   | |   ||||||||  |    |||| |  |    ||  ||||| | |||||| | || ||||| ||||||||||||||||| ||||||||||| || ||||| ||       |||||    | || | |||   |   |  
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAA-GGACCGAAAGGCCACTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA
                                 ttcttgcattctct  CT-rich tract
                       taacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagttactaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA