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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcaggcaaataccgtttggtcctcatgtccctgtccctgacacagtttccctaaccaaccgcctgttcctgtatacgtaaatagtcatgtctctcttctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT

Basic information

species Zea mays
transcript GRMZM2G158489_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158489_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g09000.1 (Oryza sativa), 3'ss of exon 9
gtttgttcaggcaaataccgtttggtcctcatgtccctgtccctgacacagtttccctaaccaaccgcctgttcctgtatacgtaaatagtcatgtctctcttctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT
           ||  |  | |    | ||  |   |    |  ||  | | ||| ||  || |||    | ||  ||| |                   | ||||   ||||||||||| ||||||||| ||||| |  | || |||||||  || ||| ||||||||||  |||||| |||||| || ||  | |||||||||||||| ||
--------gtacatgtctcataaaatgcttcttggctctcctgtggtataatttaccatactaacgaaatctttttgtgt-------------------tattcttctgcagAATGGCAAGTCTGGCTCATACTCTTATCTCTTTTCCTAGTGTCAGCCATCCTGTTCTATATGTTCTACGAGCGCTCCGATTCCTTCTGGAACTTTCCAAT
















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|149105792|gb|EE291382.2|EE291382
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|211501284|gb|FL248092.1|FL248092
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|71308208|gb|DR790336.1|DR790336
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|32837118|gb|CD976796.1|CD976796
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGT
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGT
EST: gi|76010774|gb|DT937944.1|DT937944
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|89251668|gb|DY623454.1|DY623454
EST:     TCAGTGGGGGGCGGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|89760375|gb|DY688809.1|DY688809
EST:     TCAGTGGGGAGCGGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCTTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|211501285|gb|FL248093.1|FL248093
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCACTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|78079988|gb|DV508400.1|DV508400
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|6021240|gb|AW066168.1|AW066168
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCACTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|211411697|gb|FL434955.1|FL434955
EST:     TCAGTGGGGAGCACAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|93017687|gb|EB643207.1|EB643207
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|88757842|gb|DY541983.1|DY541983
EST:     TGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTATTCCTGGCGCTCTTCTTAGCCTCCGCCGTCC
genomic: TGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|86474634|gb|DY241004.1|DY241004
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|78115282|gb|DV533670.1|DV533670
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|76287602|gb|DV027170.1|DV027170
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|71596195|gb|DR906946.1|DR906946
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCACTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|16921161|gb|BM075014.1|BM075014
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|91053037|gb|EB163455.1|EB163455
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|74237401|gb|DT645315.1|DT645315
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTTTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|50329947|gb|CO525073.1|CO525073
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|86470686|gb|DY237056.1|DY237056
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|74236583|gb|DT644497.1|DT644497
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|211115136|gb|FL479369.1|FL479369
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|88748364|gb|DY532505.1|DY532505
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|32938162|gb|CF042981.1|CF042981
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGT
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGT
EST: gi|6445478|gb|AW179396.1|AW179396
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCACTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
EST: gi|76020754|gb|DT947924.1|DT947924
EST:     TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAG                         AATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC
genomic: TCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCC

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: 43 (upstream exon), 46 (downstream exon)
Score: 60

GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 52

GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 46

GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 24

GGTTGTAATCTCCACATCACATCAGTGGGGAGCAGAGCTCACGAAACTGAACGTGCCTGCCGACTGGAAAGgtttgttcag ... tctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccaaccgcctgttcctgtatacgtaaatagtcatgtctctcttctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT
 ccctaac  putative branch site (score: 24)
                                 tcatgtctctcttctc  putative PPT
                          taaatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcaggcaaataccgtttggtcctcatgtccctgtccctgacacagtttccctaaccaaccgcctgttcctgtatacgtaaatagtcatgtctctcttctctggcagAATGGCAGGTCTGGCTCGTACTCCTGGCGCTCTTCCTAGCCTCCGCCGTCCTGTTCTACGTGTTCTTCGAGCGATCAGACACGTTCTGGAACTTTCCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCGCCG