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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaatagtcgattggtgttacttggactgttcaagaaactacaggatgtgatttagttagatattgttctaatcgaatctttccaaatggtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG

Basic information

species Zea mays
transcript GRMZM2G028535_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 18
-------------------------------------aacaatagtcgattggtgtt---acttggactgttcaagaaactacaggatgtgatt------tagttagatattgttctaatcgaatctttccaaatggtttgcgaa----gGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG
                                      |   | ||  | | ||  |   |     |  |||   |||| || | | ||| | |      | || ||   ||  |  | ||   | ||| |      ||  | ||    |||||||||||| |||| |||||||||||| || || |||||||| ||||||||||| ||||| ||||| ||
gtatgtcctttaaatttgtatcactttataacttggacattttcgttaactagttatcaaaaaaaaatagttatcgaaaatatatgttgttactattgaatggtcagcgtttcattcagtcccctattttctttcctttatcaaatatagGTTGGCATAAGCACAGGGCGCATACATGCTCGGGGGCCTGTTGGCGTTGATGGACTCCTAACAACTCGATG
















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|60344250|gb|DN211223.1|DN211223
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|67017479|gb|CO446228.1|CO446228
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|6564250|gb|AW231872.1|AW231872
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|6022040|gb|AW066983.1|AW066983
EST:     ATGCAAGCNCAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|211181079|gb|FL441227.1|FL441227
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|101391685|gb|EB817779.1|EB817779
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGCCCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|6564119|gb|AW231741.1|AW231741
EST:     ATGCAAGCCCAAGGTTTTGTGATGGGACGCGTTTTGGGTTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|149066719|gb|EE286860.2|EE286860
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|211181077|gb|FL441225.1|FL441225
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAG                         GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT
genomic: ATGCAAGCACAAGGTTTTGTGATGGGACGCGTTTTGGGCTAGGTGCTGAGgtactttctt ... gtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgatttagttagatattgttctaatcgaatctttccaaatggtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG
                      ttctaat  putative branch site (score: 2)
      atttagttagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaatagtcgattggtgttacttggactgttcaagaaactacaggatgtgatttagttagatattgttctaatcgaatctttccaaatggtttgcgaagGTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA