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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcatgctttacctagctattcatttccaaatacatgcaggtcttctgtaagggcactgtttatgattttttgttgttgttgttgttgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGAGAGAACTTAAAAGCATGTGCTGTTTTCCATGGGGATGCAGCATTCAACG

Basic information

species Zea mays
transcript GRMZM2G151905_T03
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151905_T05 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os07g49260.1 (Oryza sativa), 3'ss of exon 22
gtatagcatgctttacctagctattcatttccaaatacatgcaggtcttctgta-agggcactgtttatgattttttgttgttgttgttgttgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGAGAGAACTTAAAAGCATGTGCTGTTTTCCATGGGGATGCAGCATTCAACG
                        | | ||   ||||  |  |  || | |  | |    | | | | || |    |  | |    |||     | |  |||||||||| || ||||||||||| ||| | || ||||||    || ||||||| ||||||||||||||||| |   |||| ||||| ||  | ||||| |
-----------------------gtaagttattaatagttttaattcatttccatatactagtttatctggtcacataatttgacagttcactct-atcagGTAAAGGACTCGGATCCTATCAAGCAAGCTTCTCTAGAGGACATGCTAAGAGATAACTTAAAAGCATGTGCAGCACTCCACGGGGACGCGACTTTCAATG
















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|76015952|gb|DT943122.1|DT943122
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|37361410|gb|CF602699.1|CF602699
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|6020477|gb|AW065405.1|AW065405
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTGGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|211283755|gb|FL354685.1|FL354685
EST:     ATGGTTCAGGTTACTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGKGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|32837283|gb|CD976961.1|CD976961
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|32839265|gb|CD978946.1|CD978946
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|5739723|gb|AI947299.1|AI947299
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|60342170|gb|DN209143.1|DN209143
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|32837177|gb|CD976855.1|CD976855
EST:     AAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: AAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|5762205|gb|AI967253.1|AI967253
EST:     TTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: TTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|6563769|gb|AW231301.1|AW231301
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
EST: gi|32837702|gb|CD977380.1|CD977380
EST:     ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG                         GTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA
genomic: ATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAGgtatagcatg ... tgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctgtaagggcactgtttatgattttttgttgttgttgttgttgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGAGAGAACTTAAAAGCATGTGCTGTTTTCCATGGGGATGCAGCATTCAACG
                  tttatgattttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcatgctttacctagctattcatttccaaatacatgcaggtcttctgtaagggcactgtttatgattttttgttgttgttgttgttgttgactagGTAAAGGATTCAGATCCTATCAAACAAACATCGCTAGAGATGGTGTTAAGAGAGAACTTAAAAGCATGTGCTGTTTTCCATGGGGATGCAGCATTCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT