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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttatttgaaatctcattacattattttgtgcatctaccatttttttgtatgcacatataggtaatgcttgctggcaacttgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 8
gtattttatttgaaatctcattacattattttgtgcatctaccatttttttgtatgcacatataggtaatgcttgctggcaacttgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
                   |||   |           ||     |||| |||| |  |    || ||||   ||  |||  |||||||||| ||||||||||| || |||||||||||||||||||||||| ||||| | 
-----------------gtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
















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|76929603|gb|DV172080.1|DV172080
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|60342784|gb|DN209757.1|DN209757
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTAC
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTAC
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|149103005|gb|EE288366.2|EE288366
EST:     ATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: ATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|37621887|gb|CF674940.1|CF674940
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGA
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGA
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|76018526|gb|DT945696.1|DT945696
EST:     CGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: CGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAA                         GACTGATAGCGCATT
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATT
EST: gi|78023022|gb|DV491409.1|DV491409
EST:     ATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: ATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|110944605|gb|EE164762.1|EE164762
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTG
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     GTTCCTGGGGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAG                         GGCTGATAGCGCATTGAA
genomic: GTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAA

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: 48 (upstream exon), 34 (downstream exon)
Score: 165

GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 283

GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 227

GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 454

GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatt ... tgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatttttttgtatgcacatataggtaatgcttgctggcaacttgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA
                                           cttgtttt  CT-rich tract
     tttttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttatttgaaatctcattacattattttgtgcatctaccatttttttgtatgcacatataggtaatgcttgctggcaacttgttttgcagGACTGATAGCGCATTGAAGTTTGGATTGTTCTTCTTGCTTTACGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG