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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctgagttaccaaggttgtgcag

Basic information

species Zea mays
transcript GRMZM2G063792_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 9
GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcag
||| ||||||||||||||| |||||||| ||||||||||||||||| || |||||||| |||||||||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   ||||
GACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcag

upper sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 5'ss of exon 8
-----------------------------------GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatggg----accttggcttcatttggcat-gtacaagtaccaggggatctgagttaccaaggttgt-gcag
                                   ||| ||||||||||||||| |||||||| ||||||||||||||||| || |||||||| |||||||||||||  ||||    |  || | ||  | |   ||   |  |  | ||||   | |||||||| || | |   ||||
ATGTTTACGATTGGAATGGCTGTTGTTCTGTTCAGGACTTGGATGGAGTTACCCCTGTGATATATGGAGTGTTGGTTGTATACTGGTTGAGCTATGCACGgtatgttgttgggtgcaatatttggtttgtattctatcacaacaacagcaggatttttgagttacgaaagctaccgcag

upper sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA17G13440.1 (Glycine max), 5'ss of exon 7
-----------------------------------GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctga----gttaccaaggttgtgcag-----------
                                   ||| ||| ||||| || |||||||||||||||||||| || |||||  | |||||| | |||||||||||||       |          | |   |   | |  || |      |  ||     || |  |  ||||| |            
GCAAGCTAAAGTTGATTTTGGCAATGATGTTTTAGGACTTGGCTGGAGCTATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacag

upper sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA17G13440.2 (Glycine max), 5'ss of exon 8
GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctga----gttaccaaggttgtgcag-----------
||| ||| ||||| || |||||||||||||||||||| || |||||  | |||||| | |||||||||||||       |          | |   |   | |  || |      |  ||     || |  |  ||||| |            
GACTTGGCTGGAGCTATCCATGTGATATCTGGAGTGTGGGATGTATCTTGGTTGAGTTATGCACGgtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacag

upper sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 5'ss of exon 9
GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatg-ttaatgggaccttggcttca-----tttggcat-gtacaagtaccaggggatctgagttaccaaggtt--gtgcag-------------------------
| | |||||||||||| |||||||| || ||||| |||||||||||  | || || || ||  ||||||| |||||    |  | |  | |      || ||||   |    |    ||  ||    || |  |||      ||||                          
GGCTTGGATGGAGTTATCCATGTGACATGTGGAGCGTTGGTTGTATATTGGTGGAACTATGTTCGgtatgcttaatctctctgtagtattaatgatctttgcatcaaatggctggatggtaatacatgtcatgaagtcctaatgcaaaacatgtggctgcttcctgttgcag

upper sequence: GRMZM2G063792_T06 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 5'ss of exon 9
GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctgagttaccaaggttgtgcag---------------------
| | |||||||||||| ||||||||||| ||||||||||| |||||  | || ||| | ||||||||| ||| ||   |  |    | || |     |   |   |      ||   ||   |    ||||| ||  |                     
GGCTTGGATGGAGTTATCCATGTGATATATGGAGTGTTGGATGTATCTTGGTGGAGTTATGCACGgtacgtttat--taattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggttatgatgcaacatttattcattacacag

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|32804365|gb|CD956601.1|CD956601
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|33104273|gb|CF064233.1|CF064233
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32804851|gb|CD957087.1|CD957087
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|113698224|gb|DW851180.1|DW851180
EST:     GTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: GTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32794020|gb|CD946256.1|CD946256
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|4776116|gb|AI665119.1|AI665119
EST:     AGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCNCGAAAACTTGGAACATCTGGCTATGATG
genomic: AGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|7162469|gb|AW520091.1|AW520091
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
EST: gi|32802406|gb|CD954642.1|CD954642
EST:     ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACG                         GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG
genomic: ACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATG

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: 27 (upstream exon), 49 (downstream exon)
Score: 264

GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAGT


Block sizes: 27 (upstream exon), 46 (downstream exon)
Score: 175

GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAGT


Block sizes: 27 (upstream exon), 48 (downstream exon)
Score: 200

GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAGT


Block sizes: 27 (upstream exon), 48 (downstream exon)
Score: 259

GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaat ... ggttgtgcagGGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATGGATGGAGTTACCCATGTGATATCTGGAGTGTTGGTTGTATTCTTGTTGAGCTTTGCACGgtatgttaatgggaccttggcttcatttggcatgtacaagtaccaggggatctgagttaccaaggttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT