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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacaccttgaaccgatgccttctctggcggttttattcggatctgtttcagccgggggtttcactcgtttggattcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG

Basic information

species Zea mays
transcript GRMZM2G147882_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 6
gtaa-tacaccttgaaccgatgccttctctggcggtt---ttattcggatctgtttcagccggg-ggtttcactcgtttggattcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG
|||| | || |||||| |||  |||| ||    | ||   | |||    |   ||  |       |||     ||  |  || |  |||||||||||||||||| ||| |||||||||||| | |||||||| ||||||||  | |||||
gtaaatgcatcttgaatcgacaccttatcaaatgtttcattgattttcgtgacttctaataaaatggtagttttccatctgaattatgcagATATGCAAGGACAGGAATGCTCAGCCTCAAGTATGGGAATATGTAGCTCCTGTAAAAGG
















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|78077655|gb|DV506089.1|DV506089
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925957|gb|CF030769.1|CF030769
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926415|gb|CF031227.1|CF031227
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926466|gb|CF031278.1|CF031278
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|74241069|gb|DT648983.1|DT648983
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926635|gb|CF031447.1|CF031447
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926849|gb|CF031661.1|CF031661
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|71437198|gb|DR818248.1|DR818248
EST:     CTACGGCCTGATAACTCTCCTGGGCA-CCGATGATGTAGTTGGGCTCAAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGGATACGTAGCTCCG
genomic: CTACGGCCTGATAACTCTCCTGG-CAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926430|gb|CF031242.1|CF031242
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926417|gb|CF031229.1|CF031229
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925395|gb|CF030207.1|CF030207
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|76287315|gb|DV026883.1|DV026883
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGNCAGGGACA-GAACGCTCAGCCTCAACTGTGGGAATACGTAG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATG-CAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAG
EST: gi|71758494|gb|DR956431.1|DR956431
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926166|gb|CF030978.1|CF030978
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926025|gb|CF030837.1|CF030837
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|71299018|gb|DR785501.1|DR785501
EST:     ATTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGTTCAGCTTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925152|gb|CF029964.1|CF029964
EST:     ACTACGACCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|71429425|gb|DR810475.1|DR810475
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|76287314|gb|DV026882.1|DV026882
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     CTACGGCCTGATAACTCTCCTNGGCA-CCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: CTACGGCCTGATAACTCTCCT-GGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926219|gb|CF031031.1|CF031031
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|78078283|gb|DV506698.1|DV506698
EST:     ATTACGGCCTGATAACTCTCTTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32858735|gb|CD998416.1|CD998416
EST:     GTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: GTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926072|gb|CF030884.1|CF030884
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926162|gb|CF030974.1|CF030974
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32926197|gb|CF031009.1|CF031009
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925587|gb|CF030399.1|CF030399
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925272|gb|CF030084.1|CF030084
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925426|gb|CF030238.1|CF030238
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
EST: gi|32925266|gb|CF030078.1|CF030078
EST:     ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAA                         ATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG
genomic: ACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCG

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: 39 (upstream exon), 35 (downstream exon)
Score: 10

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 288

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 15

TAAGGTGTCAGATCCTGCAAAGGGTGTTTACGGAGCGGGCGCCCATTCAGACTACGGCCTGATAACTCTCCTGGCAACCGATGATGTAGTTGGGCTCCAAgtaatacacc ... attcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggttttattcggatctgtttcagccgggggtttcactcgtttggattcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG
                                              ttcctgc  CT-rich tract
     ttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatacaccttgaaccgatgccttctctggcggttttattcggatctgtttcagccgggggtttcactcgtttggattcctgcagATATGCAAGGACAAGAACGCTCAGCCTCAACTGTGGGAATACGTAGCTCCGTTGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC