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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actttccatatatctattttttcagtccttttgttttactttggttggttgtcagcaccagcattgtttggttagttatagcttttctgttgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAGCGAGATCAGTAT

Basic information

species Zea mays
transcript GRMZM2G484880_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g01130.1 (Oryza sativa), 3'ss of exon 8
--actttccatatatctattttttcagtccttttgttttactttggttggttgtcagcaccagcattgtttggttagttatagcttttctgttgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAGCGAGATCAGTAT
  |   |   |  |||   | | || |||    | ||||        |   | |          |        | |    | |  ||  |  |||  ||||||||||||||||| |||||||||||| |||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| | | | ||||| 
aaaacctatttgcatcatctgtgtctgtcaagattttttttaaaaaatatatatttttcttgaaaagacccactaaaactttgtattgtt--tgtactgaagGATAAATGACTCTTATGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAACAACAGCAGTAC

upper sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g34300.2 (Oryza sativa), 3'ss of exon 8
--actttccatatatctattttttcagtccttttgttttactttggttggttgtcagcaccagcattgtttggttagttatagcttttctgttgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAGCGAGATCAGTAT
   | |    | | ||| |       ||  ||||     |  ||  ||  |  | |  |    ||||      ||   ||| | || |   ||||  ||||||||||||||||| || ||||||||| |||||||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||| | ||||| 
ttgcatcatctgtgtctgtcaagcttgtttttttaaaaaatatttatttttcttgaaaagacccattaaaactttg--tattgtttgtactttgtactgaagGATAAATGACTCTTACGCTGAGATTTTGAAAGGATTGCGATGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTGTATAAGAAAGAGCGACAGCAGTAC

upper sequence: GRMZM2G484880_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv18s0001g09710.t01 (Vitis vinifera), 3'ss of exon 7
----actttccatatatctattttttcagtccttttgttttactttggttggttgtcagcaccagcattgtttggttagttatagcttttctgttgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAGCGAGATCAGTAT
      |||| || ||| || || |       ||||  | ||   | ||  ||  |  ||   |   ||   ||  || || ||     | ||||||    |||||||  ||| ||   ||  || ||||||||||| ||||| || |||||||| ||||||||||| |  |||||| | ||| | |  |||||  | ||||||
atgtcatttctat-tatgtaattataattaaattttaatatataattgtatgtaatttgc--taaattttaatgtataattgtatggaatttgttgtac-aaagGATATCTGATTCGGCTGGAGAAATTCTGAAAGGGTTACGTTGTTACTTTGACAAAGCATTGCCAGTGATGCTTCTGTATGAAAGGGAGCGTCAACAGTAT

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|60343282|gb|DN210255.1|DN210255
EST:     GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|78544095|gb|DV621593.1|DV621593
EST:     GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|31997933|gb|CD661838.1|CD661838
EST:     GATGATATTCTAAAGAAGTACTTGGAACNCCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|211056265|gb|FL131318.1|FL131318
EST:     ATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: ATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|37386752|gb|CF630565.1|CF630565
EST:     GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGTTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|33103032|gb|CF062992.1|CF062992
EST:     ACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: ACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|211399030|gb|FL440153.1|FL440153
EST:     ATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: ATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|22546503|gb|BU098814.1|BU098814
EST:     GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|22546502|gb|BU098813.1|BU098813
EST:     TGGAACCCCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: TGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|93284202|gb|EB676466.1|EB676466
EST:     GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
EST: gi|5917408|gb|AW054199.1|AW054199
EST:     GATGATATTCTAAAGAAGTACTTGGAACNCCGGGCAAAGAAGGATGGCAA                         GATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA
genomic: GATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAAgtgagtattc ... tgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttgtcagcaccagcattgtttggttagttatagcttttctgttgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAGCGAGATCAGTAT
                                    cttttctgtt  CT-rich tract
                          ttagttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actttccatatatctattttttcagtccttttgttttactttggttggttgtcagcaccagcattgtttggttagttatagcttttctgttgtgttgaagGATAAATGACTCCTATGCTGAGATTCTGAAAGGATTACGCTGCTACTTTGATAAAGCATTGCCTGCAATGCTTTTATATAAGAAAGAGCGAGATCAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - ttggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caccagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg