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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgcccttcccgttagcgtttgtgtttccttattcgtcttgtttgtggcgcgccgaatgggtttcgggatcacggaatttgtcgttgttcacgcgacgcgttatgacttacgcgcgtgcttgcttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA

Basic information

species Zea mays
transcript GRMZM2G085747_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g35960.2 (Oryza sativa), 3'ss of exon 2
gtgagtcgcccttcccgttagcgtttgtgtttccttattcgtcttgtttgtggcgcgccgaatgggtttcgggatcacggaatttgtcgttgttcacgcgacgcgttatgacttacgcgcgt-gcttgcttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA
                          |||  ||      ||||   || |  |         | |    || ||||||   || | |  |  ||  |   | | |   ||   | |||  |  |||||||  ||| |||||||||| ||| |||||||||||||||| ||||| || ||||| ||| ||||||||||||||||||| |||||||||||||||||| |||||||||||||
--------------------------gtgagtctac-cccgtccacttcgccgaattt----tcgcccgcgagatcacctgatatctgctgctttgcctaatgtggcgtgtgatgcgcttgccgcttgctgtgttgcagTAAACTCGTTCAGGTCGCTGGAGCACAACACCCGGGGAGAGCCCGACACCATCGTCGCGCTGGCCAAGTGGAGGATCCTCAACAGGCTGCACGACCGGAA
















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|76919658|gb|DV167819.1|DV167819
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211274711|gb|FL015918.1|FL015918
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211274712|gb|FL015919.1|FL015919
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|71437509|gb|DR818559.1|DR818559
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211016654|gb|FL375789.1|FL375789
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|29130557|gb|CB381261.1|CB381261
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|29130494|gb|CB381198.1|CB381198
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|149102281|gb|EE287658.2|EE287658
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211384290|gb|FL369291.1|FL369291
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211048980|gb|FL422995.1|FL422995
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211527375|gb|FL402913.1|FL402913
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCA
EST: gi|211272913|gb|FL015917.1|FL015917
EST:     CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTA                         TAAACTCTTTCCGGTCGCTGGAGCACAATACCC
genomic: CTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCC

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), 47 (downstream exon)
Score: 126

GATACGGCGTTCCCCATGACGGAGCGCGACCGCCTCGGTCTCCGCGGCTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 77

GATACGGCGTTCCCCATGACGGAGCGCGACCGCCTCGGTCTCCGCGGCTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GATACGGCGTTCCCCATGACGGAGCGCGACCGCCTCGGTCTCCGCGGCTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 85

GATACGGCGTTCCCCATGACGGAGCGCGACCGCCTCGGTCTCCGCGGCTTGCTCCCGCCGCGGGTCATGTCCTTCGAGCAGCAGTACGAGCGATTTAgtgagtcgcc ... ttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcgttgttcacgcgacgcgttatgacttacgcgcgtgcttgcttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA
                          gacttac  putative branch site (score: 85)
                                        cttgcttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgcccttcccgttagcgtttgtgtttccttattcgtcttgtttgtggcgcgccgaatgggtttcgggatcacggaatttgtcgttgttcacgcgacgcgttatgacttacgcgcgtgcttgcttcgttacagTAAACTCTTTCCGGTCGCTGGAGCACAATACCCGCGGCGAGCCTGACTCCATCGTCGCGCTGGCCAAATGGAGGATCCTCAACAGGTTGCACGACCGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT