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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgcacccagctttgttatttgagcatatttatatattggactgctctgttggaacgaattttctacactctgaacttctgaagcatacagaatattttgtatatccatttgacaattatgttctgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG

Basic information

species Zea mays
transcript GRMZM2G104166_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104166_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g45670.1 (Oryza sativa), 3'ss of exon 7
gtatgtatgcacccagctttgttatttgagcatatttatatattggactgctctgttggaacgaattttctacactctgaacttctgaagcatacagaa-tattttgtatatccatttgacaattatgttctgattga--tagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG---
|||||||| |  |||||  | ||        | |||| | |       ||  ||||||  ||       | |||| |||      | |||  | ||||| |  | | |  ||| | || |  ||||| || ||||||   |||||||| || ||||| ||||| ||||||||||| ||||| ||| |||| |||||||| ||  |||  |||   |||||||||||||| ||| | |||||     
gtatgtatac-tccagcactatt-------tacattttttttaaaacatggcctgttgacacag----cccacacactg------tcaagtgtgcagaagtcctatcttcatcaagttaatgattattttttgattggtttagATGGTATCAGAGCGTCAAAAGATTGAAGCACCTCCGACCCCATCAGCAGAAAATTACATGGCACAGCCA---CCACCATCTTATGACGAAGTCAATGGCATGT
















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|211163115|gb|FL067004.1|FL067004
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAATAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|67017186|gb|CO445935.1|CO445935
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|78543553|gb|DV621051.1|DV621051
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCNNNNNNNTTGAAGCACCCCCGACTCCAGCAGCTGA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCC-AAAAAATTGAAGCACCCCCGACTCCAGCAGCTGA
EST: gi|20301506|gb|BQ164449.1|BQ164449
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTCGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCNNNNNNNTTGAAGCACCCCCGACTCCAGCAGCTGA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAA-TTGAAGCACCCCCGACTCCAGCAGCTGA
EST: gi|6095746|gb|AW120413.1|AW120413
EST:     AACTTACCATCAGAGAGTTCTGGAGAATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: AACTTACCATCAGAGAGTTCTGGAG-ATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|211163116|gb|FL067005.1|FL067005
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|211163114|gb|FL067003.1|FL067003
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|5895761|gb|AW037007.1|AW037007
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|91053809|gb|EB164227.1|EB164227
EST:     GGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|26456480|gb|CA828063.1|CA828063
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCC
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCC
EST: gi|91056506|gb|EB166924.1|EB166924
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|5847057|gb|AW000136.1|AW000136
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|76283089|gb|DV022657.1|DV022657
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
EST: gi|148996412|gb|EE035707.2|EE035707
EST:     GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAA                         ATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA
genomic: GAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAA

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: 46 (upstream exon), 44 (downstream exon)
Score: 84

GTTGAGGCTGAGAGAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 380

GTTGAGGCTGAGAGAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 402

GTTGAGGCTGAGAGAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 373

GTTGAGGCTGAGAGAACTTACCATCAGAGAGTTCTGGAGATACTTGACAAATTGGAAGAAGAAgtatgtatgc ... tgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagcatacagaatattttgtatatccatttgacaattatgttctgattgatagATGGTGTCTGAGCGCCAAAAAATTGAAGCACCCCCGACTCCAGCAGCTGAAAATTATATACCACCACCAGCACCACCATCTTATGATGAAATTAATGGAG
                                          ttctgat  putative branch site (score: 373)
          agaatattttgtatat  TA-rich tract