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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaaaataaatttacatatcttcttctgtatttctggccttgtatttaaacagttgaattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT

Basic information

species Zea mays
transcript GRMZM2G118917_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118917_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 3'ss of exon 12
gtaagaaaaaataaatttacatatc---------------ttcttctgtatttctggccttgtatttaaacagttgaattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT
||||| ||||  || | | | |||                 | ||      |  |     ||||||| |||   || ||||| |||| |||||| || || |||||||| |||||||| |||||||||||||||||||| || || ||  || || |||||||||| | | | |||||   ||| |
gtaaggaaaataaactattcctataaaaaaggggaaaaaactgtttaaatctgttattgctgtatttgaacgactgcattatgcagGTAGCAAAAGCCACAGTTCAAGTGTCAAAGAGACCTACAGCTTTTGGAGCTCTATTAGGGAAACCAACTTCTGGAAGAAGACAAAACCTTTTTTCAGGGT
















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|32933312|gb|CF038124.1|CF038124
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTCAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|60337067|gb|DN204040.1|DN204040
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTCAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|26456572|gb|CA828155.1|CA828155
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|211193425|gb|FL343339.1|FL343339
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGAAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|20301496|gb|BQ164439.1|BQ164439
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|211301949|gb|FL333158.1|FL333158
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGAAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|60396058|gb|DN228927.1|DN228927
EST:     AGACAACAAAAAGCTGAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
genomic: AGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
EST: gi|211248404|gb|FL329614.1|FL329614
EST:     GGTTTACTGGACTGACAGACAACAAAAAGCTCAGCAATGACCAGCAGCAA                         GCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT
genomic: GGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCT

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), 49 (downstream exon)
Score: 341

GCATTTAGAGGACCCTGTGCCTAAAACAAAGGACTCGGGTGCTTCATCAGGGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 137

GCATTTAGAGGACCCTGTGCCTAAAACAAAGGACTCGGGTGCTTCATCAGGGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GCATTTAGAGGACCCTGTGCCTAAAACAAAGGACTCGGGTGCTTCATCAGGGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GCATTTAGAGGACCCTGTGCCTAAAACAAAGGACTCGGGTGCTTCATCAGGGTTTACTGGACTGACAGACAACAAAAAGCTGAGCAATGACCAGCAGCAAgtaagaaaaa ... aattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatatcttcttctgtatttctggccttgtatttaaacagttgaattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT
                               tatttaaacagttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaaaataaatttacatatcttcttctgtatttctggccttgtatttaaacagttgaattatacagGCAGCAAAGGCTACTGTTCAAGTATCAAAGAGGCCTACAGCTTTTGGAGCTCTGTTTGGAAAGGCAGCTGCTGGAAGAAGGCCAGATCTTTTCCTAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG