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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtcgggttcttcattccattgaggataccatacacgttttactacatcctcagattattgcaatattgttcgcttactttccttaatgaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG

Basic information

species Zea mays
transcript GRMZM2G134888_T01
intron # 8
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134888_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g01100.2 (Oryza sativa), 3'ss of exon 9
acagtcgggttcttcattccattgaggataccatacacgttttactacatcctcagattattgca-atattgttcgcttactt------tccttaatgaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG
     ||   |  |||  | |       |   || ||   |||||   |  || | | |||||   |||| | ||    |  |       ||||||  ||||| |||||||||||| || || |  |||||||||||||||||||||||  ||||||| ||||| || || |||||| | |  ||||||||||||||||| || |||
----acgaaattctcaaactacaattattcatat-catactttacatga--ctgaaactattgtggatatggctcttcgatctgggatacccttaacaaataatcacATATGCATTGACCATAACCCCATTGGCTATGAGTTTGGAAGAATTGCTGCCTCCAAATCAGCAGAAGTATGCGAACATAATCATGCTTAGATCCTCCCTG
















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|78105407|gb|DV523825.1|DV523825
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|78107412|gb|DV525830.1|DV525830
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|78107411|gb|DV525829.1|DV525829
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|94477484|gb|EB706442.1|EB706442
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|71774552|gb|DR972430.1|DR972430
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|37375777|gb|CF624353.1|CF624353
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|211253075|gb|FL452728.1|FL452728
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
EST: gi|149101391|gb|EE187509.2|EE187509
EST:     CAACGGTGGCAAATCCAATAACCAA                         ATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC
genomic: CAACGGTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 49 (downstream exon)
Score: 12

GTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 34

GTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 11

GTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG


Block sizes: 20 (upstream exon), 47 (downstream exon)
Score: 17

GTGGCAAATCCAATAACCAAatatccttgg ... gaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcctcagattattgcaatattgttcgcttactttccttaatgaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG
                                    ttccttaat  putative branch site 
           attattgcaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtcgggttcttcattccattgaggataccatacacgttttactacatcctcagattattgcaatattgttcgcttactttccttaatgaataaacacATATGCATTAACTATTATTCCATTGGCTATGAGTTTGGAAGAGCTGCTGCCACCAAACCAACAAAAGTATTCTACAATAATCATGCTTAGATCATCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - cattcca
- - - - - - - - - - - - - - - -catacac
- - - - - - - - - - - - - - - - - - - - - - ctacatc