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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgctgggcacttgcagaaaattgtttgttagtgtcatcatcttgtggccaggcattatgctatataactgatgaggtgttgtcctgacccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG

Basic information

species Zea mays
transcript GRMZM2G001645_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001645_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g31970.1 (Oryza sativa), 3'ss of exon 3
-tatgctgggcacttg-cagaaaattgtttgttagtgtcatcatcttgtggccaggcattatgctatataactgatgaggtgt--tgtcctgacccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG
 | |   |  ||| ||   || | || |   ||||  |  | ||||| ||       |||||  |||| || |||||||||||  |||  | ||| |||  ||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||||||||| |||||||| || || || ||||||||||| || || || || |
ctgtagggaacacctggtggacatttatgcattagcat--ttatcttatgtttgccaattata-tata-aattgatgaggtgttctgtgataaccaaaatgcagGTGGGCACGGTTGGTGGAGGCACACAGCTGGCCTCACAGTCTGCTTGCTTGGACCTACTTGGCGTGAAGGGCGCAAACAGGGAATCCCCAGGATCAAATG
















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|71300000|gb|DR786070.1|DR786070
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|22935926|gb|BU572201.1|BU572201
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|149105213|gb|EE290700.2|EE290700
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|60343183|gb|DN210156.1|DN210156
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|28188237|gb|CB179847.1|CB179847
EST:     TAAATGATGACAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|76018248|gb|DT945418.1|DT945418
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|71763156|gb|DR961093.1|DR961093
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|30086988|gb|CB885196.1|CB885196
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|148929661|gb|EC876184.2|EC876184
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTATTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|149042497|gb|EE047180.2|EE047180
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|71448863|gb|DR829913.1|DR829913
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|88747943|gb|DY532084.1|DY532084
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|71420176|gb|DR805036.1|DR805036
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTTCTATGCCATTTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|101389504|gb|EB816690.1|EB816690
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|67011977|gb|CO440726.1|CO440726
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|149085519|gb|EE175029.2|EE175029
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|74233110|gb|DT641024.1|DT641024
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|91873059|gb|EB403016.1|EB403016
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|60348632|gb|DN215605.1|DN215605
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|87156121|gb|DY400910.1|DY400910
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|71769556|gb|DR967493.1|DR967493
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|71430350|gb|DR811400.1|DR811400
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
EST: gi|78114303|gb|DV532692.1|DV532692
EST:     TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAG                         GTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG
genomic: TAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTG

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: 49 (upstream exon), 49 (downstream exon)
Score: 69

CCCTGCACAGAACGTGGAGAGTTCCCAGTGCATCACCATGTTGGAAGCTATAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 121

CCCTGCACAGAACGTGGAGAGTTCCCAGTGCATCACCATGTTGGAAGCTATAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

CCCTGCACAGAACGTGGAGAGTTCCCAGTGCATCACCATGTTGGAAGCTATAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 142

CCCTGCACAGAACGTGGAGAGTTCCCAGTGCATCACCATGTTGGAAGCTATAAATGATGGCAAAGATCTCCACATCTCTGTTACTATGCCATCTATTGAGgtttgaaaca ... ccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggccaggcattatgctatataactgatgaggtgttgtcctgacccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG
                                      tcctgac  putative branch site (score: 142)
          attatgctatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgctgggcacttgcagaaaattgtttgttagtgtcatcatcttgtggccaggcattatgctatataactgatgaggtgttgtcctgacccaaacacagGTTGGCACAGTTGGTGGAGGCACGCAGCTGGCCTCACAATCTGCCTGCTTGGACCTGCTTGGCGTCAAAGGTGCCAACAGGGAATCTCCGGGGTCCAACG

tatgctg
- - - - - acttgca
- - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - gccaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatga