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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtctagagcttgtggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcag

Basic information

species Zea mays
transcript GRMZM2G025231_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 5'ss of exon 8
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtctagagcttg-----tggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcag
||||||||||||||| ||||| ||||| || |||||| | || ||||| || |||||||| || ||||| || ||||| |||||||||||||| |||||||| | | || |||| ||     || | | || || ||   |  |||||| | |||  |||| ||| |||| |  | || |       
TGGTGGAACCTTGAAAAGTGCGAGTCCAGCATCTCTTCTAAAGGAAGCAATTCATGTCATAAGCTGTGGGTACGAAGATAAGACAGACTGGGGGAAAGAGgtaaggactggagcctgattgctgttaactggttaattgattgaaacatttcttaactagttaattatatctt-tgttgcag-----

upper sequence: GRMZM2G025231_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA06G47420.1 (Glycine max), 5'ss of exon 16
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgt---gaagtctagagcttgtggttattgctttatgagtcaaaacatatg--ttagatagtgaatcatatgtc---atcttacttttcag--------------------
|||||  ||  | ||   || ||  | ||||||||   | | |||||| |||||||||||||||||||| |||||||| || ||||| ||||||||||||||   ||| |||    |   |  | | |   || |     ||  | | |   | |  | || | |  || |     ||   ||| |  |                     
TGGTGAGACACTCAAACATGGAAACCTTGCTTCTCAACTTACAGAAGCAATACATGTCATTAGTTGTGGCTATGAAGAGAAAACAGAATGGGGAAAAGAGgtaatgaaatcttt--ccattaatcactatgttcttctctaagtcttcttgctcaagttgtaacttgtaagcatggattcaactctaaaaaaattcctttaattgctcag

upper sequence: GRMZM2G025231_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 5'ss of exon 12
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtctagagcttgtggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatct--tacttttcag-------------------
|||||||||  |||| | ||| |||||||| ||||| || || |||||||| ||||| ||||| |||||||||||||| || || ||||||||||||||||| || | | ||  | |    | ||||      || ||   ||| |    |||  | | |    | | || |  ||||  | |                    
TGGTGGAACACTGAAAATTGCGAGTCCTGCATCTCTATTAAAGGAAGCTATCCATGTGATTAGCTGTGGTTATGAAGATAAAACGGACTGGGGAAAAGAGgt-aactatggatatggcttgttttgcccc-caagacatttcattttggggattct-atttggttattatttagtactggtaaattttattaagaaagaaaga

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|211310943|gb|FL374710.1|FL374710
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|88752891|gb|DY537032.1|DY537032
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|211121712|gb|FL408178.1|FL408178
EST:     TTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|211147734|gb|FL419640.1|FL419640
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|32916441|gb|CF021253.1|CF021253
EST:     TGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|211219468|gb|FL394125.1|FL394125
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|32850633|gb|CD990314.1|CD990314
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|32941882|gb|CF046701.1|CF046701
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|211275142|gb|FL390045.1|FL390045
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|71324690|gb|DR799051.1|DR799051
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG
EST: gi|211159525|gb|FL378589.1|FL378589
EST:     TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAG                         ATGGGCTGGATCTATGGATCAGTTACAGAAG-TATTCTAACTGGTTTCA-G
genomic: TACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAG

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), 49 (downstream exon)
Score: 66

TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 57

TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 758

TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtcta ... tacttttcagATTGGCTGGATCTATGGATCAGTTACAGAAGATATTCTAACTGGTTTCAAGATGCATTGTCATGGTTGGCGGTCAATTTACTGCATACCTAAACGGGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGAACCTTGAAGAGTGCAAGTCCTGCTTCTCTTTTGAAAGAAGCTATACATGTCATTAGTTGTGGTTATGAAGACAAGACAGACTGGGGAAAAGAGgtgaagtctagagcttgtggttattgctttatgagtcaaaacatatgttagatagtgaatcatatgtcatcttacttttcag

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