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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattagttaatactgcttcacctttcgcatgcacatcccttaggtttcacgagtagtgtaattttgcagcctaacatgattctcaccattatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGG

Basic information

species Zea mays
transcript GRMZM2G095782_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095782_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g19954.2 (Oryza sativa), 3'ss of exon 2
taattagttaatactgcttcacctttcgcatgcacatcccttaggtt-tcacgagtagtgt--aattttgcagcct-aacatgattctcaccattatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGG
  || |  ||   ||  || || ||  |  || ||||| || ||  | | |  || | |    ||||||| |  || || |   |    || || || | |||||||||||||||||||||||   |||||| ||||||| |  | | ||| ||||||| | | ||||||| ||||||||||| ||| | || ||||| || ||
--ataaactac--cttgttgacattatgtgtgaacatcactgagactgtgatcagaacttcagaattttgaaatctcaataatctaactacaatcatgtttcagGTTGGCAGTATCAACCATCGCCTCCAACCATACAATGTAGTATTGAGAATGCGCTAACACGCATCACAAAGCTGGATCGCAAGGAGCTCTGCTTGGTTGG
















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|32839977|gb|CD979658.1|CD979658
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAA                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|89249529|gb|DY621315.1|DY621315
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAG                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|101390146|gb|EB817005.1|EB817005
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAAC-AAGTTCAAAG                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|32835800|gb|CD975478.1|CD975478
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAA                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|32835822|gb|CD975500.1|CD975500
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAA                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|33468040|gb|CF245089.1|CF245089
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAG                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|37423784|gb|CF649621.1|CF649621
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAG                         GGTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|101391179|gb|EB817523.1|EB817523
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCCAAG                         GTTGGCAGTATCAACCATCAATTCCCAACAATACAATATTTTCTAGAGGA
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCC-AACAATACAATATTTTCTAGAGGA
EST: gi|32839936|gb|CD979617.1|CD979617
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAA                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|76013636|gb|DT940806.1|DT940806
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAAC-AAGTTCAAAG                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
EST: gi|91876899|gb|EB406856.1|EB406856
EST:     CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAG                         GTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG
genomic: CATGCACAAGTGGAGGATGGTCATCGCCTACGATGGAACAAAGTTCAAAGgtttgatttg ... tatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcacgagtagtgtaattttgcagcctaacatgattctcaccattatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGG
                                   ttctcac  putative branch site (score: 2)
            tgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattagttaatactgcttcacctttcgcatgcacatcccttaggtttcacgagtagtgtaattttgcagcctaacatgattctcaccattatatctcagGTTGGCAGTATCAACCATCAATTCCAACAATACAATATTTTCTAGAGGATGCGCTGATATGCATCACTAAGCTGGATCGGAAGAAACTATGCTTAGTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA