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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcgagggatccattaaccttctcctctgtgcttcgttttccccttgcaaagtgctactctggaactggtaaaaacgacacgatcagcatttaga...

Basic information

species Zea mays
transcript GRMZM2G047274_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047274_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g58580.1 (Oryza sativa), 5'ss of exon 1
TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcgagggatccattaaccttctcctctgtgcttcgttttccccttg-caaagtgctac--tctggaactggtaaaaacgacacgatcagcatttaga-
||||||||||||||||| || ||||| |||||||| |||||| |||||||||||||||| |||||||||||||| ||| ||||||||||||| |||||||||||| ||| |   |       ||||| ||| |||| |   || | || ||  || | || | |  ||   ||   ||||||   |   | |||   ||  |  
TACAGCGGCCACGGCACCCGTCTGCCCGCCGAGACAGGGCAGAACGACGACACCGGCTATGACGAGTGCATCGTTCCCAGCGACATGAACCTTATCACAGgtgcgatcgggaactg----gcccttcccctttgtgttcttttctacctttatcatactgttgcaatcgataagctgtaaaagttaggagttcaaagttgtgtg

upper sequence: GRMZM2G047274_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0085g01030.t01 (Vitis vinifera), 5'ss of exon 1
TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcgagggatccattaaccttctcctctgtgcttcgttttccccttgcaaagtgctactctggaactggtaaaaacgacacgatcagcatttaga
||||||||||||||||| || || || |||||||| ||  || ||||||||||||||||||||||||||||||| ||    |||||||| || || || |||       |   || | |    | | |||        || |  |   ||   |   ||  |  |   || |  | |    |||  | |  |  || || 
TACAGCGGCCACGGCACTCGACTCCCTGCCGAGACCGGAGAGGACGACGACACCGGCTACGACGAGTGCATCGTCCCTACTGACATGAATCTTATTACCGgtcaaaatcacaaattcttctttcatttccctctcatctcatcgttttctctaattctgggagcc--aaagtaatgactgtgac--ggtttgttttcag-
















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|60354986|gb|DN221959.1|DN221959
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|149008208|gb|EE040377.2|EE040377
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|148981273|gb|EE027550.2|EE027550
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|74240878|gb|DT648792.1|DT648792
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|26557757|gb|CA829992.1|CA829992
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|211308824|gb|FL142432.1|FL142432
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAA
EST: gi|211308823|gb|FL142431.1|FL142431
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTTCAGGG
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTT-CAGGG
EST: gi|40287025|gb|CK327417.1|CK327417
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAANGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|211310846|gb|FL142436.1|FL142436
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTC
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTC
EST: gi|148955850|gb|EC901544.2|EC901544
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|42492002|gb|CK701048.1|CK701048
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|67014949|gb|CO443698.1|CO443698
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|149102341|gb|EE188191.2|EE188191
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
EST: gi|71759363|gb|DR957300.1|DR957300
EST:     CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAG                         ATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA
genomic: CACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 47

TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCACCATCGTCTCTGACTCATGCCATAGTGGTGGCCTGCTGGACAGTGCTAA


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

TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCACCATCGTCTCTGACTCATGCCATAGTGGTGGCCTGCTGGACAGTGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCACCATCGTCTCTGACTCATGCCATAGTGGTGGCCTGCTGGACAGTGCTAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 137

TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcga ... caatctgcagATCAGGATTTCAGGGAACTCGTGCAGAAGGTCCCTGAAGGTTGCCTATTCACCATCGTCTCTGACTCATGCCATAGTGGTGGCCTGCTGGACAGTGCTAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACAGCGGCCACGGCACGCGCCTGCCAGCCGAGACGGGGCAGCACGACGACACCGGCTACGACGAGTGCATCGTGCCCTGCGACATGAACCTCATCACAGgtgcggtcgagggatccattaaccttctcctctgtgcttcgttttccccttgcaaagtgctactctggaactggtaaaaacgacacgatcagcatttaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaacga