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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatcacaacttagttttatatactttatgcttgaattgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

Basic information

species Zea mays
transcript GRMZM2G136296_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
cttatcacaacttagttttatatactttatgcttga-attgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttc---agATTGTTAATGGACCTCGC---TCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC
   | | ||  |||||  |  |    ||| | |  | ||| |||||  ||| | |||||  |   | | | ||    | | | | ||| |    || ||   ||||||| |||||||||||     |||||  ||||| | |||||||||||||||||||||| || ||||||||||||||||| || ||||| ||||||||     
---aac-cattttagtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA---

upper sequence: GRMZM2G136296_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA05G33320.1 (Glycine max), 3'ss of exon 15
cttatcacaacttagtt--ttatatactttatgcttgaattgccgttattagctcctggtc-gttctagaaattttattattgtct----tcatgtggt-ttgttcagATTGTTAATGGACCTCGC---TCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC
        ||    |||  | | || |   ||  |   | || || |  || | ||| ||| ||||    ||  ||| |  | | |    |  | |||  ||||  || | || |||||||||||     |||| ||||||| |||||||| |||||||||||||||||| || ||||| || ||||| |  || || |||  ||  |   
--------aatagggttgatgagatgcaaaatagtcagagtgtcgcttgtaccacctagtctgttcagtcaaacttacttctttatgaaatggtatggaattgtgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTCCAAACGACATGTTTGAAGTATTCTATATTGATTATGGAAATCAAGAAGAAGTACCTTACTCTCAGC---
















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|511415|gb|T23393.1|T23393
EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGTAAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
EST: gi|67011396|gb|CO440145.1|CO440145
EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
EST: gi|211486828|gb|FL010663.1|FL010663
EST:     AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATG                         ATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA
genomic: AGATAGTCCTCTCACAATTTAGCCTTGACAACTCCTGGAACAGAGCTATGgtatgtcgca ... gtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC
                                              tttgttc  CT-rich tract
               ttctagaaattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatcacaacttagttttatatactttatgcttgaattgccgttattagctcctggtcgttctagaaattttattattgtcttcatgtggtttgttcagATTGTTAATGGACCTCGCTCTGTAGAATCTCTAAACGACAAGTTTGAAGTATTCTATATCGACTATGGCAACCAAGAGGTGGTTCCCTACAGTCGTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- -atcacaa
- - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - -gctcctg