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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGAGGCCGGCATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctttaatttctcctctactagtactacacgtctacactgtaactcccaccagaccacaccactgcgtctgcgtgcttgatgcttcattatcttgcgtgtgtgtcactggctaacctgtggggctacttcacgtctccttggtgtggttgcgtgcactgcacag

Basic information

species Zea mays
transcript GRMZM2G103055_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103055_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g52710.1 (Oryza sativa), 5'ss of exon 2
GGATGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGAGGCCGGCATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtt-tgctttaatttctcctctactagtactacacgtctacactgtaactcccaccagaccacaccactgcgtctgcgtgcttga-tgcttcattatcttgcgtgtgtgtcactggctaacctgtggggctacttcacgtctccttggtgtggttgcgtgcactgcacag
|| ||||||||||||||||||||||||||||||||||||||||  ||||||||||| |||||||||||||||||| |||| |||||| ||| |||||||||||   |||| |  | ||||     |     || |       |||  |  |   ||  | ||     ||   |||     ||||||| ||||||   |                                                                          
GGGTGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGCAGCCGGCATCACCCACGTCTGGCTCCCTCCGCCGTCTCACTCTGTCGGCGAGCAAGgtgcggtgctctgctctctcgatccc-----ctccgtcgtcgcaccattgccggcaaaatacatgcacaggtcgttgaattgcttgaatgcttctgcag-------------------------------------------------------------------------

upper sequence: GRMZM2G103055_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g52700.1 (Oryza sativa), 5'ss of exon 2
GGATGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGAGGCCGGCATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctttaatttctcctctactagtactacacgtctacactgta-actcccaccagaccacaccactgcgtctgcgtgcttgatgcttcattatcttgcgtgtgtgtcactggctaacctgtggggctacttcacgtctccttggtgtggttgcgtgcactgcacag
|| ||||||||| | ||||||||||||||||||||||||||||  ||||||||||| |||||||||||||||||| |||| || ||| ||||||| ||||||     |  |  | ||||    ||          ||||  |  |  | | | ||  || |  | | |      |  || || ||| || |                                                                                
GGGTGGTACAACATGCTGATGGGCAAGGTGGACGACATCGCCGCCGCCGGCATCACCCACGTCTGGCTCCCTCCGCCGTCTCAATCTGTCGCCGAACAAGgtc----cggtgctctctcgagcaccttcgtcgt-cgtcgtcgatccatattgccggcaaaatatatcca---attggcttgattgctgatctgcag--------------------------------------------------------------------------
















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|149071201|gb|EE159597.2|EE159597
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|76919418|gb|DV167705.1|DV167705
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|71303727|gb|DR787972.1|DR787972
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|211148615|gb|FL264741.1|FL264741
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|211148619|gb|FL264745.1|FL264745
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCCTGCCGGGGCGCC
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACC-TGCCGGGGCGCC
EST: gi|211150054|gb|FL264746.1|FL264746
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|211150055|gb|FL264747.1|FL264747
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|148949094|gb|EC894522.2|EC894522
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|71426058|gb|DR807108.1|DR807108
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|149082569|gb|EE171764.2|EE171764
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|148936111|gb|EC880173.2|EC880173
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|211148617|gb|FL264743.1|FL264743
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|211148616|gb|FL264742.1|FL264742
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
EST: gi|211148618|gb|FL264744.1|FL264744
EST:     CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAG                         GCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG
genomic: CATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACG

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 2 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 30 (downstream exon)
Score: 7

GGATGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGAGGCCGGCATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACGAGGCGCAGCTCAAGTCCCTGATCGAGGCGTTCCACAGCAAGGGCGTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GGATGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGAGGCCGGCATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctt ... cactgcacagGCTACCTGCCGGGGCGCCTGTACGACCTTGACGCGTCCAAGTACGGCAACGAGGCGCAGCTCAAGTCCCTGATCGAGGCGTTCCACAGCAAGGGCGTGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGTACAACTTCCTGATGGGCAAGGTGGACGACATCGCCGAGGCCGGCATCACGCACGTCTGGCTCCCTCCGGCGTCACACTCTCTCGCCGAGCAAGgtgtttgctttaatttctcctctactagtactacacgtctacactgtaactcccaccagaccacaccactgcgtctgcgtgcttgatgcttcattatcttgcgtgtgtgtcactggctaacctgtggggctacttcacgtctccttggtgtggttgcgtgcactgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG