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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA

Basic information

species Zea mays
transcript GRMZM2G314679_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g21250.1 (Oryza sativa), 3'ss of exon 2
ttgtttccgataaaaaaatatgaaa-acggtaatggttttagtgtttaccgaccgtttcc--gaccgttttaatccctattcagtgat-atgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
 || ||  | | |  ||  ||||||  | | | |   |  |   ||| | | || || |     |   | ||||   |  | | ||   || |  ||| |||||||||||||||||||||||||||||||||| ||||||||||||||||| || |||||||| || || || ||||| ||||||||| | | |||||| ||||
-tgcttttgttgatgaa-catgaaatgcagcattaagt--aactttttctgtcctttgcacaagctcatgtaatgattcatgattgtccattttcgttacacagGAATCTTGCCCTTCTGTGAAGAACATTTTGCTTCTGGATTCTGAAGGGAAACGTGTTGCCGTGAAATACTTCTCGGATGATTGGTCTAGTAATGCGTCAA

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT3G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgtttt------aatccctattcagtgat------atgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
                              | || | |  | | ||  | || |    |      |  ||  | ||       ||||    |  ||||          | || | | |||       ||||   ||  | |||| ||||| ||||  || ||||| ||| | ||||| || ||||||||||||||||| ||||| ||||||| ||| ||||| ||||| ||||||||  | |
gtaagtacatatgcattatatgattgtatttcgtattctgttagaatgtgtgtatgttgccgcaatcatacagctttgtaggagttttactctttttttggactggaacttaattactgactttccaatgtacattgaatagGATTCTTGTCCTTTGGTAAAGAAGATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCGGATGACTGGCCAACTAATGCCGCCA

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT4G08520.1 (Arabidopsis thaliana), 3'ss of exon 2
-ttgtttccgataaaaaaat--atgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
   |||     | | |  ||  ||   || | |  | | ||  |  | | |    | | ||  |    ||  || |  | |   || | |      |  | |||| ||||| ||||  || ||||||||| | ||||| || ||||||||||||||||| ||||| ||||||| ||| ||||||||| | |||||||| || |
gaagttcaaacttacatgatccattttaaggattctcgcttctgcttgtgcttctc-tctcttagtacttacatgctgactatctggtcta--caatgaatagGATTCTTGTCCTTTGGTAAAGAACATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCCGATGATTGGGCAACTAATGCTTCCA

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcac--------agGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
    || |  |  |   ||       | || |    |||  || ||   ||   ||||      | ||||||  |||||  |  | ||| |   | ||        ||||||    |||    ||||| ||||| || ||| |||||||||||||||||||||| || || ||||||| ||||||||| ||||| || ||| || |  
----ttactgttcactgattcatgttctgttacatcttt--tggttggtgat--tttcaatatctcttaatctttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 3'ss of exon 1
ttgtttccgataaaaaaatatgaaaacggtaatggtttta--gtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA---
 |  || | ||         |      ||  |||  || |   |||| |  |     |||  | |  || |     | ||  ||  | | | | ||| | |||   ||||||| ||| | || |||||| | ||||||||||||||||| |||||||| || || || |||| ||| ||||||||||| || |||||  |||   
-ttctttcaatcttttttattttgtttggacatgcattcatcatgttaattgttttcttctaatcaattcagattttgttttgttttgt-tttcttttatagG---CTTGCCCCTCTATAAAAAACATTCTTCTTCTGGATTCTGAAGGGAAGCGTGTGGCAGTCAAATATTACTCCGATGATTGGCCAACAAATGCTGCAAAAT

upper sequence: GRMZM2G314679_T05 (Zea mays), 3'ss of exon 2
lower sequence: Vv10s0003g02760.t01 (Vitis vinifera), 3'ss of exon 2
--------ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
        |    |     |     || |   |   | |     |||||| || |   ||      || |   | | ||   |||  | |  | | | | ||||| |||| || ||||||||||| || |||||| | || ||||||||||||||||| ||||| ||||| ||||| |  |  || || ||||| || |||    | |
aaacaaattcaaatttatcattcctatgtagtagttg-agcacatttagttttcatgaact-----cgcctagtctgatatttatgtaat--tttttttttttcatagGAGTCATGCCCTTCTGTAAAAAACATTCTCCTCCTGGATTCTGAAGGAAAACGTGTAGCTGTCAAGTACTATTGTGACGACTGGCCAACAAATAATGCTA

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|31357552|gb|CD441909.1|CD441909
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184335|gb|FL140041.1|FL140041
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211181937|gb|FL140035.1|FL140035
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|87157301|gb|DY402090.1|DY402090
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|7137590|gb|AW499170.1|AW499170
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184344|gb|FL140050.1|FL140050
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|15313043|gb|BI478532.1|BI478532
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184341|gb|FL140047.1|FL140047
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|22819508|gb|BU499598.1|BU499598
EST:     GGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|56382683|gb|CV985352.1|CV985352
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184337|gb|FL140043.1|FL140043
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211344197|gb|FL190861.1|FL190861
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184338|gb|FL140044.1|FL140044
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|62550301|gb|DN830721.1|DN830721
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|5928724|gb|AW055941.1|AW055941
EST:     GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211006747|gb|FL429436.1|FL429436
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211181941|gb|FL140039.1|FL140039
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211181938|gb|FL140036.1|FL140036
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184339|gb|FL140045.1|FL140045
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|33103253|gb|CF063213.1|CF063213
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211181939|gb|FL140037.1|FL140037
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTT-ACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211181940|gb|FL140038.1|FL140038
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
EST: gi|211184343|gb|FL140049.1|FL140049
EST:     GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAG                         GAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG
genomic: GGTGGAATAGGGAACGGCCATACACCATGGCGGATTTCTCCAAGgtgcgaagaa ... tgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA
                   ttttaat  putative branch site (score: 3)
                                           tctgtttc  putative PPT
                   ttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttccgataaaaaaatatgaaaacggtaatggttttagtgtttaccgaccgtttccgaccgttttaatccctattcagtgatatgtctgtttcacagGAATCTTGCCCTTCTGTGAAGAACATTTTACTTCTGGATTCTGAAGGAAAGCGTGTTGCTGTAAAGTATTTCTCAGATGATTGGCCGACTAATGCATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG