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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttccggctctttttatttctccgtggtttattatatattagcagcacgctgttaattaattaattaattaatcgccgggtcttttatatatgtttgtgtgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG

Basic information

species Zea mays
transcript GRMZM2G000842_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000842_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g37170.4 (Oryza sativa), 3'ss of exon 11
gtttccggctctttttatttctccgtggtttattatatattagcagcacgctgttaattaattaattaattaatcgccgggtcttttatatatg-tttgtgtgac-cagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG
      | | |     ||   |   |  || | || | |   |||  |   |          ||| |  ||   |      | |||| | |||| ||||  |    || |||||||||||||| |||||||| || ||  |||||| ||||||||| ||||||| ||  ||||| | ||||||||||||||||||||||||||||| |||||
---gtagacacacaacataattttttttttcagta-agacacgcacgattattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttcaccagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG
















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|71760398|gb|DR958335.1|DR958335
EST:     AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTCCTGAAATCCTCAAG                         ATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
genomic: AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
EST: gi|88758004|gb|DY542145.1|DY542145
EST:     AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAG                         ATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
genomic: AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
EST: gi|91869978|gb|EB400638.1|EB400638
EST:     GGGAGGGTTCCGTCCTTCTGAAATCCTCAAG                         ATGCGGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
genomic: GGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
EST: gi|71757092|gb|DR955029.1|DR955029
EST:     AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAG                         ATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
genomic: AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
EST: gi|88753493|gb|DY537634.1|DY537634
EST:     AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAG                         ATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
genomic: AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
EST: gi|74246417|gb|DT654331.1|DT654331
EST:     AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAG                         ATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG
genomic: AGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATG

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 3 RNA-Seq libraries.


Block sizes: 20 (upstream exon), 33 (downstream exon)
Score: 3

AAGATCCGACGTGTTCCACCTGATGACCGGCCTGTGGGCGACCACGGCCGAGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG


Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1

AAGATCCGACGTGTTCCACCTGATGACCGGCCTGTGGGCGACCACGGCCGAGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG


Block sizes: 37 (upstream exon), 40 (downstream exon)
Score: 10

AAGATCCGACGTGTTCCACCTGATGACCGGCCTGTGGGCGACCACGGCCGAGCGATGCTTCCTCTGGATGGGAGGGTTCCGTCCTTCTGAAATCCTCAAGgtttccggct ... tgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaattaattaattaatcgccgggtcttttatatatgtttgtgtgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG
            aattaat  putative branch site (score: 10)
     attaattaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttccggctctttttatttctccgtggtttattatatattagcagcacgctgttaattaattaattaattaatcgccgggtcttttatatatgtttgtgtgaccagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG