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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcatctttgccaatttattctgtaacatgcaaatgcaatccttcattatcttttcttatgttttgacgtgtatgctaatggttctcttccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC

Basic information

species Zea mays
transcript GRMZM2G037200_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g45480.4 (Oryza sativa), 3'ss of exon 5
catcatctttgccaatttattctgtaacatgcaaatgcaatccttc-attatcttttcttatgttt-tgacgtgtatgctaatggttctcttccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC
 |||  | ||||  |   |||  | |||| |||    |  | ||||  | |  |||  | || |   |  |   |   || |||| | | ||  | ||  |||| ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||| |||||||||||||||||||  ||||||| ||||||||
-atctgccttgcacaaa-atttggaaacacgcatgccctttacttctgtcaaatttcttcatttcaatttccaatgctctgatggctttgttttatctgtagGGAGCACTTGCCCTAAGTGGCATGCCTGATGCACAATCAAAACCTGTGCTACTATGTTCACTAAATGACAACACTGTCCGACTATATGACCTGCCATC
















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|211273334|gb|FL390033.1|FL390033
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|211495269|gb|FL457209.1|FL457209
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACMCAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|29576813|gb|CB616925.1|CB616925
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|149095549|gb|EE181206.2|EE181206
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|149086360|gb|EE175901.2|EE175901
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|211403681|gb|FL424159.1|FL424159
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|60347714|gb|DN214687.1|DN214687
EST:     CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
EST: gi|211527293|gb|FL400210.1|FL400210
EST:     CTACAGAGAGTGGAAACTTAGAAGYAACATATACACACAAAGAGGATCAG                         GGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA
genomic: CTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTA

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), 46 (downstream exon)
Score: 158

GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 146

GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GTTTGGGCCGCTACAGAGAGTGGAAACTTAGAAGTAACATATACACACAAAGAGGATCAGgtataaggcc ... ccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatcttttcttatgttttgacgtgtatgctaatggttctcttccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC
                             tgctaat  putative branch site (score: 177)
                                      ttctcttccaccttc  putative PPT
       ttttcttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcatctttgccaatttattctgtaacatgcaaatgcaatccttcattatcttttcttatgttttgacgtgtatgctaatggttctcttccaccttcagGGTGCACTTGCCCTCAGTGGTATGCCTGACGCACAGTCAAAACCTGTGCTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC

- - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggttct