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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcagtgtttattcattttccatccaaatcatccagatataggttgcatcagagattcatagttggctatctattgcatgtagttaaatacacagtcatgttgttatctcttctgttattgaagtgttttgtatcttagagtccaactgcattactgacataaatgcccctcttctattgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA

Basic information

species Zea mays
transcript GRMZM2G087144_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087144_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g35960.1 (Oryza sativa), 3'ss of exon 2
gtaagtgcagtgtttattcattttccatccaaatcatccagatataggttgcatcagagattcatagttggctatctattgcatgtagttaaatacacagtcatgttgttatctcttctgttattgaagtgttttgtatcttagagtccaactgcattactgacataaatgcccctctt--ctattgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA--
||||||    || ||||  ||||    |  | ||   |   |||| | || ||  |||     ||| ||| |||| | ||   | |  | ||| |   || ||| |   ||    |  | ||       |||| || ||||||    |  || |  | | | | |||   |||  | ||  || ||||  |||||||||||| || | || ||||||||||||||||||||||| ||||||  
gtaagtt---tgattatctattt---gtttagatgtcctgcatat-gtttaca--aga-----atacttgcctat-tgttttgtttgttcaaagatttagacatata--tagtagtgatattgaaagcatgttctgcatcttact-ccgtacagtctaattaatatactggccttttttttctgttgtgtcagGGCATTGAACCAGGAATCAGGGCTGAAGTTTGGCCCTTCCTGCTAGGAGT
















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|148981030|gb|EE027393.2|EE027393
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCCAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|149106092|gb|EE291756.2|EE291756
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|148939166|gb|EC883612.2|EC883612
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|50332287|gb|CO527413.1|CO527413
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTACGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|211397522|gb|FL373465.1|FL373465
EST:     GGAAGCTTCGTGATGGTGGGAGGGAGTTTCTCAAGAAAGNTCGCAGTGGT                         GGCATGGAAGCAAG-ATTTAGGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATT-AGGG-CTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|211328212|gb|FL409834.1|FL409834
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|211240372|gb|FL028808.1|FL028808
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|211240371|gb|FL028807.1|FL028807
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|211476313|gb|FL383250.1|FL383250
EST:     AAGCTTCGTGATGGTGGAANGGAAAGTT-CTCA-GAAAGT-CGCAGTGGT                         GGCATTGAAGCA-GCATTAGGGCTGAAGTTTGCCCCT
genomic: AAGCTTCGTGATGGTGGAA-GGAA-GTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCT
EST: gi|50325323|gb|CO520449.1|CO520449
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
EST: gi|148959376|gb|EC905424.2|EC905424
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCC-TTCCTACTAGGA
EST: gi|148964953|gb|EE015802.2|EE015802
EST:     GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGT                         GGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
genomic: GGAAGCTTCGTGATGGTGGAAGGAAGTTTCTCAAGAAAGTTCGCAGTGGTgtaagtgcag ... attgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttagagtccaactgcattactgacataaatgcccctcttctattgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA
                     tactgac  putative branch site (score: 1)
                                 tgcccctcttctatt  putative PPT
                          acataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcagtgtttattcattttccatccaaatcatccagatataggttgcatcagagattcatagttggctatctattgcatgtagttaaatacacagtcatgttgttatctcttctgttattgaagtgttttgtatcttagagtccaactgcattactgacataaatgcccctcttctattgtaccagGGCATTGAAGCAAGCATTAGGGCTGAAGTTTGGCCCTTCCTACTAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG