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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattcagtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtag

Basic information

species Zea mays
transcript GRMZM2G005036_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 5'ss of exon 4
TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattcagtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtag
 ||||||| ||||||||| ||||| ||||||||||||||||||||||||||||| || || ||| | |||||||||   | |||||||||||| ||| |||||||| | ||| ||||||    || || |||  |||||||   | || ||| | | ||  |||      || |      |  ||| ||||||||
CCATTCGGCTGGATATTCTGGGGCTCTGGCAAAACCTTTGATGGCTTCAGAATCCGCGGTGAACAGATTGGATGTTGCTACCTTGGAGGAATTCGTTTCTgtaagactaagttatttat----catgttaatagtcagtcacagatgcctctgtttcaccctttgac--attcttgcttgtgctgagaaatgtag
















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|31356317|gb|CD440674.1|CD440674
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|89761459|gb|DY689465.1|DY689465
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|31358559|gb|CD442916.1|CD442916
EST:     AATCTGCTGTAAACCGGGTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|88755226|gb|DY539367.1|DY539367
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|71438038|gb|DR819088.1|DR819088
EST:     GGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: GGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|19822381|gb|BQ048405.1|BQ048405
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|30031572|gb|CB833423.1|CB833423
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
EST: gi|211246196|gb|FL443898.1|FL443898
EST:     AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCT                         GAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT
genomic: AATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattca ... ataaatgtagGAACATTACACTGCTCCCAGGATGGTTCTTGCAGCATCAGGAGTTGATCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATTCGGTTGGATATTCCGGGGCACTGGCAAAACCTTTGATGGCTTCAGAATCTGCTGTAAACCGGTTGGATGTTAGCAGCTTGGAGGAATTTGTTGCTgtaagattcagtgatttatttcccaagtcaatgctcagtcatgaaagcgtctctgtgacttttttgtttgttatgataaattatgataaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA