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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaactttttgactgccttgattcattcaaagtagcagtgatattaccatcttgggactaccatttttttttaaattctgcttaagtcaattaagc...

Basic information

species Zea mays
transcript GRMZM2G157310_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 5'ss of exon 7
TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagta-actttttgactgccttgattcattcaaagtagcagtgatattaccatcttgggactaccatttttttttaaattctgcttaagtcaattaagc----
||||||| |||||||||||||| || ||||| ||||||||||| ||| | || |||||||||||| |||||||||| |||||||| ||||||||||| |||| |||| ||||  | |    |||| ||  | |  |  |    |    ||| | |||     || |   | |   |||  || | |  | |  |  ||  |    
TGAAGAAGAGGACCAATGTGCTTCTCCTTGGAGATCACATTGGCGACCTTGGAATGTCTGATGGTCTAAACTATGAAAACAGGATTGCTGTTGGATTTCTgtaagtagacttccttatcatcttgctttttgcttaccatttttagatttatcttct----gctgcatctatagcttagtttatccccatgg-atctagactgta

upper sequence: GRMZM2G157310_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G33690.1 (Glycine max), 5'ss of exon 8
TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagt----aactttttgactgccttgattcattcaaagtagcagtgatattaccatcttgggactaccatttttttttaaattctgcttaagtcaattaagc
||||||| || |||||||| || || || || ||||||| ||| |||||||| |||||||||||||| || ||||| |   | ||  |  | |||||||||| |||    ||  | ||  |    || ||    |   | | ||   | ||  ||    ||   ||      |    | || |   |  ||    ||       
TGAAGAAGAGAACCAATGTTCTCCTCCTCGGTGATCACACTGGAGACTTGGGAATGTCTGATGGTTTGAATTATGAGACTCGAATATCCATGGGATTCCTgtaagttacgaatctctttgccaaatttatgttcttctaattgcttgggtaacacgtaattaatacagaggctcaactgtataaaattattgttgcag------

upper sequence: GRMZM2G157310_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv13s0073g00650.t01 (Vitis vinifera), 5'ss of exon 8
TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaactttttgactgccttgattcattcaaagtagcagtgatattaccatcttgggactaccatttttttttaaat-tctgcttaagtcaattaagc---
||||||| || |||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||||||  ||||||| |   | ||  |||| |||||||||| ||| | ||   ||||    |   ||     |  ||    |  |||| |    ||   | ||    |  |  | |||| | | |||| || |    | |   
TGAAGAAGAGAACCAATGTGCTGCTTCTTGGTGATCACATTGGAGACTTGGGAATGTCAGATGGTTTGGACTATGAAACTCGAATATCTGTGGGATTCCTgtaagttagtta--gactttgctcgatctccatatctaatcttattattgctgattt--taatatttctcctcctaaaatatatccttatgttataacaacttg

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|149013204|gb|EE042840.2|EE042840
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|71774185|gb|DR972065.1|DR972065
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|211203591|gb|FL469055.1|FL469055
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|91877197|gb|EB407154.1|EB407154
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|71763675|gb|DR961612.1|DR961612
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|149009394|gb|EE153935.2|EE153935
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|31354764|gb|CD439121.1|CD439121
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|211348037|gb|FL481321.1|FL481321
EST:     TAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: TAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|78092208|gb|DV520582.1|DV520582
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|37400710|gb|CF637712.1|CF637712
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
EST: gi|88749393|gb|DY533534.1|DY533534
EST:     GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCT                         GAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT
genomic: GGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACAT

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: 44 (upstream exon), 46 (downstream exon)
Score: 33

TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACATTGTATATCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 24

TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACATTGTATATCTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 21

TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACATTGTATATCTG


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 16

TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaact ... gattttccagGAACGCCAACATCGAGAAATCTTTGAAGGATTACTCTAGCGCGTTTGACATTGTATATCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAAAGGACCAATGTGCTGCTACTTGGCGATCACATTGGGGACTTGGGGATGTCTGATGGTTTAAACTATGACAACAGGATCGCTGTTGGATTCCTgttagtaactttttgactgccttgattcattcaaagtagcagtgatattaccatcttgggactaccatttttttttaaattctgcttaagtcaattaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT