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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagttcaaattataacatgatttccctttactttagctgcgaagaagtttgtgccttgcaaaacttattttatgtaaactgaacttgtatcttaatctgttaggtatgctttatgttccattgattgctgatgtaatgtcttctttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA

Basic information

species Zea mays
transcript GRMZM2G101874_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101874_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------gtatcagtt-caaattataacatgatttccctttactttagctg-cgaagaagtttgt-gccttgcaaaacttattttatgtaaactgaacttgtatcttaat-ctgttaggtatgctttatgttccattgattg-ctgatgtaatgtcttctttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA
                                      |||||| |||||| |  ||| |  |      ||| ||  || | | |  | || |    || |   ||   |  | | |    |||     | | | ||| ||| ||   ||    | ||||  | || ||| || ||||||||  |  ||| || ||||||||||||||||| |||||| | |||||||  ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtatgtttggatgacagcaatggaaacctctcacttagtcagttgcaaattttttcat-acctaggaacactatatatgtccatggggcttattattttactgtaccgttcatttttgttttgagtaaatttatgaattctgctaatcatatgctttgtt--agtgtttggctaatgtaatgaatggttttattctagCACTTGTTGAAACTCTGGTGGCAAAGACCAGGGCATGGGAGGAGAGCCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA

upper sequence: GRMZM2G101874_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G43450.1 (Glycine max), 3'ss of exon 15
gtatcagttcaaattataacatgatttccctttactttagctgcgaagaagtttgtgccttgcaaaacttattttatgtaaactgaacttgtatcttaatctgttaggtatgctttatgttccattgattgctgatgtaatgtcttctttc-------atcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA
                                                               | ||   |||     |  | |   || |||  |  ||  ||    ||| | |  | ||             |   ||| |||| |||        |    |||  | ||||| |   ||||  | || ||    |  ||||| ||    | ||   |||| || |  ||||||||||| |||||||| ||||||||||||||
--------------------------------------------------------------tacaatgcattaacaatggatttggctggtagat--attagtatactat-catggttttttggcatgcatgaacacaatatctttttttggtgaaaaattcagCTTTGGTTGATATATTGGTTGCTAAAACTCGTGTTTGGGAAGAAGCACCTGACATGTCATTCACATATGATGGTGTTCCTCTTCTTGCTATGTTGGATGA
















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|32931109|gb|CF035921.1|CF035921
EST:     GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAG                         CACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
genomic: GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
EST: gi|32943864|gb|CF048683.1|CF048683
EST:     GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAG                         CACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
genomic: GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
EST: gi|32931247|gb|CF036059.1|CF036059
EST:     GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAG                         CACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
genomic: GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
EST: gi|32850237|gb|CD989918.1|CD989918
EST:     GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAG                         CACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
genomic: GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
EST: gi|32930682|gb|CF035494.1|CF035494
EST:     GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGCTAACAAGATTCCAG                         CACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG
genomic: GAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTG

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: 324

GATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 35

GATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 31

GATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 59

GATGACAACAGGTATAACTCTAGCCGAGGTGCCCACCTGAATCTGAAGCGTGCAGAAAAAGCTCGTATTCTTGTTAACAAGATTCCAGgtatcagttc ... ttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaggtatgctttatgttccattgattgctgatgtaatgtcttctttcatcctagCACTTGTTGAAACCCTGGTGTCGAAGACCACAGCATGGGAGGAGAACCGTGGTCTGTCCTTTATGTATGATGGTGTACCTCTTCTAGCTATGTTGGATGA
                          tgctgat  putative branch site (score: 59)
                                     tgtcttctttcatcct  putative PPT
          tttatgtt  TA-rich tract