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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctacctttgtaacatcattccttttgactactccatctccaactttttccccacaaaaacatattgttgtttggctgtgggaatttctgctaagatttatgtaagtgtttgcattggcccctttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG

Basic information

species Zea mays
transcript GRMZM5G856598_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856598_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g63290.2 (Oryza sativa), 3'ss of exon 2
gtatctacctttgtaacatcattccttttgactactc--catctccaactttttccccacaaaaacatattgttgtttggctgtgggaatttctgctaagatttatgtaagtgtttgcattggcccctttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG
                    ||| |||||||  | |   ||      || ||||| ||||||   | || | || | ||  ||     ||| ||||   | |||| | || |  |||  |     | ||| ||| ||||||||||||||||||||| |||| |||||||| || |||||||||||||| ||||||||||||||||||||||| |||||||||||||| || ||||||
------------------gtatttcttttgatcatttatcaatcttcacgttttcgccacaa---cctaatattatgtgtttgc----attgctgccctg-tttaggaaactaattggttcaagtcttttcttatagGTGGTTTCCTCGCACAGAGCGATCAAGTGCTGTCGGGATTGCAATGGCTGGTTTTCAGCTTGGCAATACCATTGGTTTACTTCTTTCCCCTATCATCATG

upper sequence: GRMZM5G856598_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g06040.t01 (Vitis vinifera), 3'ss of exon 2
gtatctacctttgtaacatcattccttttgactactccatctccaactttttccccacaaaaa-catattgttgtttggctgtgggaatttctgctaagatttatgtaagtgtttgcattggcccctttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG
||| | |  ||   ||  |  |      |   |  |  || |   |    | | | |   | | |||||  | ||     ||| |    || || ||| |  | |  |||    |   |||  |  ||| ||  || ||||||||||  |||||  |||| || ||||| || |||||||||||||| ||||||||||||| | | |||||| |    ||| | |||||  |||||
gtaccaa--ttaccaaagttgtagaaaattgttgtttgatgtatgatagatccgcgatttacatcatatcatggtcacagtgttgtt-cttgtgttaaaagatgttgaagaaact-ttttgaactttttcttttagATGGTTTCCTCAAACAGAACGATCCAGGGCTGTTGGAATTGCAATGGCTGGATTTCAGCTTGGCAGTGCAATTGGGCTTACGCTTGCTCCAATCCTCATG
















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|71441960|gb|DR823010.1|DR823010
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
EST: gi|74244284|gb|DT652198.1|DT652198
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
EST: gi|148960604|gb|EE011229.2|EE011229
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
EST: gi|148930771|gb|EC873100.2|EC873100
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
EST: gi|71306541|gb|DR789430.1|DR789430
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
EST: gi|91877662|gb|EB407619.1|EB407619
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
EST: gi|71435182|gb|DR816232.1|DR816232
EST:     GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAG                         GTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG
genomic: GGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGG

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), 34 (downstream exon)
Score: 28

GGGCAGCTGGTCGATCTATCTGGTTGTTTCTCTTTACCAGAGTCCTGCTGGGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 30

GGGCAGCTGGTCGATCTATCTGGTTGTTTCTCTTTACCAGAGTCCTGCTGGGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 27

GGGCAGCTGGTCGATCTATCTGGTTGTTTCTCTTTACCAGAGTCCTGCTGGGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 33

GGGCAGCTGGTCGATCTATCTGGTTGTTTCTCTTTACCAGAGTCCTGCTGGGTATTGCAGAAGGAGTGGCACTCCCAAGCATGAACAACATGGTGTTGAGgtatctacct ... tttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggaatttctgctaagatttatgtaagtgtttgcattggcccctttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG
                                         cccctttatt  CT-rich tract
              taagatttatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctacctttgtaacatcattccttttgactactccatctccaactttttccccacaaaaacatattgttgtttggctgtgggaatttctgctaagatttatgtaagtgtttgcattggcccctttattacagGTGGTTTCCTCGCACAGAGAGATCTAGTGCTGTGGGTATTGCAATGGCTGGCTTTCAGCTTGGCAATACCATTGGGTTACTTCTTTCCCCAATTATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT