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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctttcatccttcattttaatacgattaaggctcttttatttatttcttgttaagcctttttttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG

Basic information

species Zea mays
transcript GRMZM2G151905_T03
intron # 21
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 21
lower sequence: LOC_Os07g49260.1 (Oryza sativa), 3'ss of exon 21
gtatcctttcatccttc-attttaatacgattaaggctcttttatttattt---cttgttaagcct------------ttttttgtt------------tgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG
|| || | | || |||| ||||| ||| ||||  |||| ||    ||  ||     | | | ||||            ||| |||||            ||||| || ||||| ||||||||||| ||| | ||||| |||  |||||||||||| |||||   |||||||||| |||||||||| || 
gtgtcatattattcttccattttgatatgattttggctattgcgcttccttaaatctttaaggcctatatcagtttcatttattgttgatacaatgatttgcagTGGTGATATTACAAGCTCTTCTTGGCTTGGCAATGATAATTCAGGTTATTCTAACAC---AAGCAAAGAGTTGAGAAAGCGACAA
















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:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|37361410|gb|CF602699.1|CF602699
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|6020477|gb|AW065405.1|AW065405
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|211283755|gb|FL354685.1|FL354685
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTACTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|32837283|gb|CD976961.1|CD976961
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|32839265|gb|CD978946.1|CD978946
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|5739723|gb|AI947299.1|AI947299
EST:     CCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATC-CAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: CCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|60342170|gb|DN209143.1|DN209143
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
EST: gi|32837702|gb|CD977380.1|CD977380
EST:     ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAG                         CGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC
genomic: ACTACTGTCATTATAGGAAGCCGTGAAGTAAAGACTGATGACGATACTAGgtatcctttc ... ttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatacgattaaggctcttttatttatttcttgttaagcctttttttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG
 ttttaat  putative branch site (score: 3)
                                      cctttttttgtttgc  putative PPT
               tcttttatttatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctttcatccttcattttaatacgattaaggctcttttatttatttcttgttaagcctttttttgtttgcagCGGCGATATCACAAGCTCTTCATGGATAGGCAACGATGGTTCAGGTTATTCCAACACTTCAAGCAAAGAGCTGAGAAAGCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA