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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactataaatgttattgtaaacttgtttcttttgattcatagaggaagaatattgttcacactggaatgcaatttccatggatgtacactccacagttttaaatatactttctattaattctactacttttaaatttcgatatctgtaatctatgctctgcactggtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGACAATTCTGATAGCATATCGTCATTAACTATGAGCTGGGAAGATGCAAAAG

Basic information

species Zea mays
transcript GRMZM2G131070_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131070_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g43560.1 (Oryza sativa), 3'ss of exon 9
gtaaactataaatgttattgtaaacttgtttcttttgattcatagaggaagaatattgttcacactggaatgcaatttccatgga-tgtacactccacagttttaaatatact--ttctattaattctact-acttttaaatttcgatatctgtaatctatgctctgcactggtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGACAATTCTGATAGCATATCGTCATTAACTATGAGCTGGGAAGATGCAAAAG
                                                                               |||| | |   |||| |   ||    |  | |     ||| ||| ||  | | || || | | |  |   ||| ||||  || ||||       |||||| ||||||||||| |  |||||||||||||||| ||||||||||||||||| || ||||||||| | | ||| ||| | || |||||| | ||||||||| | |
------------------------------------------------------------------------------tcatgaagttctcacttccttgtgcccatgaaagcggatctgttagttacatttacattcacaatctgtgttctataatg-atcctctct--caatctctc-agGCTCAACTTCTGTCACGAGATGATGAACAGGGCTCTTCTGATGATGGTGATAATTCTGATGGTAAATCCTCAGTTACCATGAGCAGTGAAGATGCATATG
















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|74240812|gb|DT648726.1|DT648726
EST:     TAGATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAG                         GCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
genomic: TAGATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAGgtaaactata ... gtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
EST: gi|211160611|gb|FL453145.1|FL453145
EST:     TAGATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAG                         GCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
genomic: TAGATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAGgtaaactata ... gtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
EST: gi|32794411|gb|CD946647.1|CD946647
EST:     GATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAG                         GCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
genomic: GATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAGgtaaactata ... gtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
EST: gi|211302442|gb|FL244048.1|FL244048
EST:     AGATCTTCTAGNCA-CATCAGACAATAGAGTACGCTTACTCATTGCTGAG                         GCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
genomic: AGATCTTCTAG-CAACATCAGACAATAGAGTACGCTTACTCATTGCTGAGgtaaactata ... gtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
EST: gi|211302444|gb|FL244050.1|FL244050
EST:     TAGATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAG                         GCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC
genomic: TAGATCTTCTAGCAACATCAGACAATAGAGTACGCTTACTCATTGCTGAGgtaaactata ... gtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactacttttaaatttcgatatctgtaatctatgctctgcactggtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGACAATTCTGATAGCATATCGTCATTAACTATGAGCTGGGAAGATGCAAAAG
                                              tctctcc  CT-rich tract
       ttttaaatttcgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactataaatgttattgtaaacttgtttcttttgattcatagaggaagaatattgttcacactggaatgcaatttccatggatgtacactccacagttttaaatatactttctattaattctactacttttaaatttcgatatctgtaatctatgctctgcactggtctctccagGCTCAACTTTTAGCACGAGATGATGAACAAGGCTCTTCTGATGATGGCGACAATTCTGATAGCATATCGTCATTAACTATGAGCTGGGAAGATGCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG