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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaatgttgggattaccattagtgtgcatattgttaagtgggttaagttataatctacctgaatatagagtatatttttttgaacatgattcat...

Basic information

species Zea mays
transcript GRMZM2G069631_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 12
TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaatgttgggattaccattagtgtgcatattgttaagtgggttaagttataatctacctgaatatagagtatatttttttgaacatgattcat
 ||||| |||||||||||||||||| |||||| ||| | ||||||| | || |||||||| ||||||||||| |||||||  |||  || ||| |  |   |||  |     |||||| |  |||  | | ||||| || ||||  |||| |  |||   ||| |        |    
CAATTTATTTCGTGTTTTTGGTTGTACTCCTGGAAGTGCGGAGGCAACCACCTTGGAAGCAAGCAGAAATCCTATGAGgtatgtctcatcttgtgggtgttattgtttatattattgtgagctggtgttatttatactcgacctacatatgggctatccctttgtatgagccgtctcc
















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|149040613|gb|EE046854.2|EE046854
EST:     CCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAG                         GCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
genomic: CCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
EST: gi|211227826|gb|FL399539.1|FL399539
EST:     CCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAG                         GCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTG
genomic: CCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTG
EST: gi|16926667|gb|BM079735.1|BM079735
EST:     CATCAACGTTGNAAGCCAGCAGAAATCCCATGAG                         GCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
genomic: CATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
EST: gi|60394838|gb|DN227707.1|DN227707
EST:     CCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAG                         GCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
genomic: CCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
EST: gi|149008174|gb|EE040364.2|EE040364
EST:     GAAATCCCATGAG                         GCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT
genomic: GAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGT

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), 48 (downstream exon)
Score: 190

TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGTGAGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGTGAGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGTGAGGAGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaa ... acccatacagGCGACAGGTTGCTGATCCAGCAAGGCCTGCACGGACTCTGACCGGTGCTGTGAGGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATTTGTTTCGTGTTTTTGGTTGTTCTCCTGAAAGCGTGGAGGCATCAACGTTGGAAGCCAGCAGAAATCCCATGAGgtccgtcaaatgttgggattaccattagtgtgcatattgttaagtgggttaagttataatctacctgaatatagagtatatttttttgaacatgattcat

- - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG