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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtattatatatagatatatatacttgctgctctcttattatctatgtttgtgctagctgctgcgctcgtatttattattattattattaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG

Basic information

species Zea mays
transcript GRMZM2G445478_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G445478_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g32910.1 (Oryza sativa), 3'ss of exon 4
gttggtattatatatagatatatatacttgctgctctcttattatctatgtttg--tgctagctgctgcgctcgtatttattattattattattaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG
            |||   |  || | ||   ||| ||    ||| | ||||| |  |   || | ||  | ||      | |  ||||||  ||    ||||||||||||  ||||||| |||||||||||| | || || |  |||||||| ||||||||||| || || ||||| || |||||||||||||||
-----------gtattactccat-tgctctttgcacttcggttaac-atgttagactttcagtttctttgttcagtccaacttatattatgttt----ccagGTAATGGCTGTTATGTCAATGTGGACCAGATTACAACCACTTTATGCTTCTAACATGTGGAATGAGGCCCTTAATAAACGACTTGGGACTGAG

upper sequence: GRMZM2G445478_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G03160.1 (Glycine max), 3'ss of exon 4
gttggtattatatatagatat-atatacttgctgctctcttattatctatgtttgtgctagctgc--tgcgctcgtatttattattattattattaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG
      | || | ||  |  | |||   ||   |   |  |||| |   |  | || | |   ||  ||   |  | ||| | | |   ||  ||     ||||||||  |  | ||||| |||||||| ||| |||||||    |||||| | ||||||||||| |||||||| ||||||||  | |||||||||
--acaaaataaacatctacttcatagttttctcgtattaatattgtaggttctggttccaagagcaatggaattctgtttctgaatggcat-gttgtgtgcagGTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAG
















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|148929994|gb|EE285845.2|EE285845
EST:     GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCA-CCTG                         GTAATGGCCATTATG
genomic: GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATG
EST: gi|78118584|gb|DV536968.1|DV536968
EST:     GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTG                         GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
genomic: GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
EST: gi|149100003|gb|EE186056.2|EE186056
EST:     GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTG                         GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
genomic: GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
EST: gi|78118583|gb|DV536967.1|DV536967
EST:     GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTG                         GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
genomic: GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
EST: gi|76931485|gb|DV172738.1|DV172738
EST:     GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTG                         GTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC
genomic: GGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCC

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), 43 (downstream exon)
Score: 43

CCGGAGCATGTGCGGGAAACCCTACGGCTACCACAACATGATATTTAGCTGGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 22

CCGGAGCATGTGCGGGAAACCCTACGGCTACCACAACATGATATTTAGCTGGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 16

CCGGAGCATGTGCGGGAAACCCTACGGCTACCACAACATGATATTTAGCTGGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 67

CCGGAGCATGTGCGGGAAACCCTACGGCTACCACAACATGATATTTAGCTGGATCGATACGGCGTCAGACAATTACCCGCCTCCTCTTGACGCCAACCTGgttggtatta ... ttaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgtttgtgctagctgctgcgctcgtatttattattattattattaatcccagGTAATGGCCATTATGTCCATGTGGACCAGACTGCAGCCGCGCTATGCTTCCAACATGTGGAACGAAGCACTTAACAAGCGACTTGGGACTGAG
                                           tattaat  putative branch site (score: 67)
                        tcgtatttattattat  TA-rich tract