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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtatgctttactttcagtcaaatctctgtgggaacttaactatagtatttgcttacacttcactgatatgtgcctttttgaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC

Basic information

species Zea mays
transcript GRMZM2G069976_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G29750.1 (Glycine max), 3'ss of exon 11
--------gtaatg-tatgctttactttcagtcaaatctctgtgggaacttaactatagtatttgcttacacttcactgatatgtgcctttttgaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC
         || || | |       |   ||  | |    |  | | |   || ||| |    ||     | || |  |||     | | | |   | | |||||||||| ||||| ||||||||||| ||  ||||||  ||||||||||||||||| |||||||| || |||||||||| |||||  || |||||     |
tttatcttctagtgctgttgaaagttgctagatagacagtttagtggaaaaaattatggg---tgagagtagttgaaggatgacaacttatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATCATATCTTAAATC

upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G40010.1 (Glycine max), 3'ss of exon 11
gtaatgtatgctttactttcagtcaaatct-ctgtgggaac---ttaactatagtatt-tgcttacacttcactgatatgtgcctttttgaatattt----agGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC
   ||  ||  | || |     | |||  | ||      ||   |||     |  ||| ||  |     |   |||    || |   |   ||  ||    ||||||||| ||||| ||||||||||| ||  ||||||  ||||||||||||||||| |||||||| || |||||||||| |||||  |  |||||     |
---attaatcttctaatgctgttgaaagttgctagatagacagtttagtggaaaaattatgggtgagagtagttgaaggatgacaactcatattcttttgtagGTGGAGGGTATGTTATATCACCAGTGAACAAAGGAAAGCAATCAGTTGTAAAGCATATGCTTGCTATTGATTGGAAATGCTGGAGATTATATCTTAAATC

upper sequence: GRMZM2G069976_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv06s0004g02720.t01 (Vitis vinifera), 3'ss of exon 11
---------gtaatgtatgctttactttcagtcaaatctctgtgggaacttaactatagtatttgcttacacttcactgatatgtgcctttttgaatattt----agGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC
         | || | |   |  |    || |  | |  |||  |||| ||    || || || |     | | || |||  | || | ||||| |   ||    ||||||||| |||||  |||| || || || || || | ||||||||||||||| ||||||||||| || || |||||||||||||  ||||||||    ||
tttttctcagcaaaggactgtgaatacccaat--atttactggaggaattt---catggt-ttagaaagtaatgcattga-gtatgacattttgcactcttttgcagGTGGAGGATATGTGGTATCTCCTGTAAACCAGGGGAAACAATCAGTTGTAAAACACATGCTTGCTATTGACTGGAAATTCTGGAGATCTTATCTACAAAC

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|32834610|gb|CD974288.1|CD974288
EST:     CCACCACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAA                         GTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAA
genomic: CCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAAgtaatgtatg ... gaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAA




















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: 105

TAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAAgtaatgtatg ... gaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAAgtaatgtatg ... gaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

TAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAAgtaatgtatg ... gaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 101

TAATTCTATACCACTCTGTTTTCCACTACAAATGTCGTCCCGAGAAAGGCTACATCCGTGCATGTCTTAAAAgtaatgtatg ... gaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaactatagtatttgcttacacttcactgatatgtgcctttttgaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC
                                      cctttttg  CT-rich tract
                                        tttttgaatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtatgctttactttcagtcaaatctctgtgggaacttaactatagtatttgcttacacttcactgatatgtgcctttttgaatatttagGTGGAGGTTATGTAATATCACCAGTCAATCAAGGAAGACAATCAGTTGTAAAGCACATGCTTGCCATAGATTGGAAATTCTGGAAGTCTTATCTGTTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG