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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaccatgtctttatctcgcaaaaaaaaaaaagatactgcgcgctcattgaaataacagcatctactatgatttttttataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCACTTGCTGCAAACCAGGTGAACTACAGCCTCATATATAGAACCCCTGAGTT

Basic information

species Zea mays
transcript GRMZM2G111954_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 6
gtttgtaccatgtctttatctcgcaaaaaaaaaa----------------aagatactgcgcgctcattgaaat--------aacagcatctactatgatttttttataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCACTTGCTGCAAACCAGGTGAACTACAGCCTCATATATAGAACCCCTGAGTT
|| ||||   ||||| |  |  |||||  |||                   |  |  | |   |||| | || |        || |  |  | |||||||   || ||  | ||||||| ||||||||||||||| |||| ||  |||||||  | || |||||||||||||||||||| |||||||||||||| ||||| || || ||||||||
gtctgtattctgtctgtggcctgcaaattaaatgttcttgtacattcctcgaattgtttcttcctcagtaaactttcattgaaataatagtttctatgatgacttcat--tcaagAGAAACGCCTTCGGGATGCATATGCGCGGATGAAGAAAAGAGGAGTTCCACTTGCTGCAAACCAAGTGAACTACAGCCTAATATACAGGACTCCTGAGTT
















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|76281356|gb|DV020924.1|DV020924
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCT
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCT
EST: gi|149077171|gb|EE165834.2|EE165834
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGT
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGT
EST: gi|148931921|gb|EC875135.2|EC875135
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
EST: gi|148935240|gb|EC879277.2|EC879277
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAAAAGCGGG
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGG
EST: gi|149063769|gb|EE157636.2|EE157636
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGG
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGG
EST: gi|149013468|gb|EE042982.2|EE042982
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
EST: gi|148972626|gb|EE023587.2|EE023587
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAACGGGGGGTTCCAC
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
EST: gi|148982464|gb|EE028329.2|EE028329
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCAC
EST: gi|149111659|gb|EE190803.2|EE190803
EST:     TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATG                         AGAAGCGCCTTCGGGATGCACATGCT
genomic: TGCTTATGAGCAAGGCCTAGTCAAGGCTGTTGGAGTCTCAAACTACAATGgtttgtacca ... tataataaagAGAAGCGCCTTCGGGATGCACATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatactgcgcgctcattgaaataacagcatctactatgatttttttataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCACTTGCTGCAAACCAGGTGAACTACAGCCTCATATATAGAACCCCTGAGTT
                  aaataac  putative branch site (score: 2)
                                       tttttttat  putative PPT
                            atctactatgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaccatgtctttatctcgcaaaaaaaaaaaagatactgcgcgctcattgaaataacagcatctactatgatttttttataataaagAGAAGCGCCTTCGGGATGCACATGCTCGCCTGAAGAAGCGGGGGGTTCCACTTGCTGCAAACCAGGTGAACTACAGCCTCATATATAGAACCCCTGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC