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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggcttctgttgcaagttaatcttgcaatgccgctgtctctcgaaatttgcttgttacctttacttttttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGTTATGGAGCTGACCTCTGAGACTGAAGAGACTACTGTCCGGAAACTTGAG

Basic information

species Zea mays
transcript GRMZM2G341271_T02
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341271_T02 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os10g41590.1 (Oryza sativa), 3'ss of exon 17
gttaggcttctgt----tgcaag-ttaatcttgcaatgccgctgtctctcgaaatttgcttgttacctttactttt-----ttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGTTATGGAGCTGACCTCTGAGACTGAAGAGACTACTGTCCGGAAACTTGAG
|||||||| || |    | || | ||  || ||| |||| ||  || | |   || || |  |||| |||  |||      ||||| | |||||||     |||||| ||| |||| |||||||||||||| ||||| |  ||||| ||||| || ||||||||||||||| | | ||| ||  | 
gttaggctgctctgaactccaggattggtcatgctatgctgccatcac-catcatgtgttcattacattttttttggttaattcagAAATGAGAGGATAAAGCTTGAGGAAGAATACGAAGAGGTGAAAAACGAAGTCAGTGAGCTAACCTCAGAAACTGAAGAGACTACTATACAGAAGCTCCAA
















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|67022115|gb|CO450864.1|CO450864
EST:     CAAACTCAGCAAAAGATATCTGAGCTGAGAGCGTTACTGGAGCACGAGAG                         GAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGT
genomic: CAAACTCAGCAAAAGATATCTGAGCTGAGAGCGTTACTGGAGCACGAGAGgttaggcttc ... cttttttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGT
EST: gi|31352135|gb|CD436492.1|CD436492
EST:     CAAACTCAGCAAAAGATATCTGAGCTGAGAGCGTTACTGGAGCACGAGAG                         GAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGT
genomic: CAAACTCAGCAAAAGATATCTGAGCTGAGAGCGTTACTGGAGCACGAGAGgttaggcttc ... cttttttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGT
EST: gi|60346497|gb|DN213470.1|DN213470
EST:     CAAACTCAGCAAAAGATATCTGAGCTGAGAGCGTTACTGGAGCACGAGAG                         GAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGT
genomic: CAAACTCAGCAAAAGATATCTGAGCTGAGAGCGTTACTGGAGCACGAGAGgttaggcttc ... cttttttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttgcaatgccgctgtctctcgaaatttgcttgttacctttacttttttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGTTATGGAGCTGACCTCTGAGACTGAAGAGACTACTGTCCGGAAACTTGAG
 agttaat  putative branch site (score: 4)
                                cttgttacctttactt  putative PPT
                                         tttactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggcttctgttgcaagttaatcttgcaatgccgctgtctctcgaaatttgcttgttacctttacttttttcagGAGTGAGAGGCGGCGGCTTGAAGAACAATATGAAGAGGTGAAAAATGAAGTTATGGAGCTGACCTCTGAGACTGAAGAGACTACTGTCCGGAAACTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA