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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttgtttctcagtgcgatgtaattggtatatgtgttttggtttttttacccatatgctcaatgtgtttctgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA

Basic information

species Zea mays
transcript GRMZM2G081188_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081188_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 11
gtaagcatttgtttctcagtgcgatgtaattggtatatgtgttttggtttttttacccatatgctca-atgtgtttctgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGA---TCAGAGTATCTGTACTCTA
|||||||  |||  |||| |||  |     |  | |       ||  || |||  ||  ||| || | |||   |||||||||||||||||||||  || ||||||| || ||||| |||||||| ||||  | || |   ||    | |    || | ||| |  ||    ||    |  || | |  |
gtaagcacctgtc-ctcactgcattaagggttttttggccccgtttattgtttatcctttattctaacatggcgttctgctgtacagGCTCATGTATTACTGCATTTCATCAATGCGTCACATGCACGGAAGCAGATG---AACTCCAGGAGATCAGATCCTTATGGAAACCCATGTAACATGGATTTCA
















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|6448429|gb|AW181195.1|AW181195
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|74240504|gb|DT648418.1|DT648418
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|148953713|gb|EC899077.2|EC899077
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|32936978|gb|CF041797.1|CF041797
EST:     TGCTCAAGGACCAAGCAAAATCAGACGACATTATCAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGGCCGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|13382066|gb|BG458741.1|BG458741
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|60339465|gb|DN206438.1|DN206438
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATCAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGGCTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|211481484|gb|FL479226.1|FL479226
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
EST: gi|60397619|gb|DN230435.1|DN230435
EST:     TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCAT                         GCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG
genomic: TGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAG

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), 49 (downstream exon)
Score: 90

CGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 170

CGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

CGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 579

CGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCCATgtaagcattt ... tgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatatgtgttttggtttttttacccatatgctcaatgtgtttctgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA
                                         tttctgct  CT-rich tract
          ttttggttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttgtttctcagtgcgatgtaattggtatatgtgttttggtttttttacccatatgctcaatgtgtttctgctgtacagGCTCATGTGCTATTGCATTTTATTAATGCATCACATGCTCGGAGACTGAAGCAGAAGCAGAAGCAGGCAAACCCTGACCGATCAGAGTATCTGTACTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC