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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcctccttatctcctttcctctggtttgctgttttgtacttgttctgattacttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG

Basic information

species Zea mays
transcript GRMZM2G158261_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158261_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g17920.2 (Oryza sativa), 3'ss of exon 1
---------------------gtttgcctccttatctcctttcctctggtttgctgttttgtacttgttctgattactt------gcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG
                     |  | | ||    | ||  | |||| |   |  |  || |  ||| |||||||| |||       |||| |||||| | |||| | || || ||||| ||||||||||| || | | |||||||||| ||||||||||||||
gttcgcttctcctgctcccccgccttcttcagcgtttctctgcctccgccctcttccttcg--cttcttctgatttctttcatgtacaagtagATGCAGGCGCCACCACGACTTTGATCGAGTTCTACTCCACCAGCTACAAGAGCTCCGCGCCATTGCCAGG
















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|211188055|gb|FK976790.1|FK976790
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|33942227|gb|CF348827.1|CF348827
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211188058|gb|FK976793.1|FK976793
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185662|gb|FK976786.1|FK976786
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185663|gb|FK976787.1|FK976787
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|50333301|gb|CO528427.1|CO528427
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185661|gb|FK976785.1|FK976785
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|5268759|gb|AI770723.1|AI770723
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185658|gb|FK976782.1|FK976782
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185656|gb|FK976780.1|FK976780
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185660|gb|FK976784.1|FK976784
EST:     G-CGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185657|gb|FK976781.1|FK976781
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211183259|gb|FK976773.1|FK976773
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211188059|gb|FK976794.1|FK976794
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185650|gb|FK976774.1|FK976774
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185652|gb|FK976776.1|FK976776
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185651|gb|FK976775.1|FK976775
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185654|gb|FK976778.1|FK976778
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|76293168|gb|DV032736.1|DV032736
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|76017214|gb|DT944384.1|DT944384
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211188057|gb|FK976792.1|FK976792
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|32909407|gb|CF014219.1|CF014219
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTATCACCTTGATTGAGTTCTACTCTACCAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|58029903|gb|CX725330.1|CX725330
EST:     GCCGGAGCTCAATCAAGGCCTCACTTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211185655|gb|FK976779.1|FK976779
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211188054|gb|FK976789.1|FK976789
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
EST: gi|211188056|gb|FK976791.1|FK976791
EST:     GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTG                         ATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA
genomic: GCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGA

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), 47 (downstream exon)
Score: 133

GGCGACGGGGCTCCGCCGCCAGGGGCTCTATACTCCTTCGGAACGCCGTGGCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 78

GGCGACGGGGCTCCGCCGCCAGGGGCTCTATACTCCTTCGGAACGCCGTGGCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

GGCGACGGGGCTCCGCCGCCAGGGGCTCTATACTCCTTCGGAACGCCGTGGCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GGCGACGGGGCTCCGCCGCCAGGGGCTCTATACTCCTTCGGAACGCCGTGGCCGGAGCTCAATCAAGGCCTCACCTACACCGACACGTTCCGTTGCGCTGgtttgcctcc ... ttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctcctttcctctggtttgctgttttgtacttgttctgattacttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG
                                   ttctgat  putative branch site (score: 51)
                        ttttgta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcctccttatctcctttcctctggtttgctgttttgtacttgttctgattacttgcaagcagATGCGGACGCCGCTACCACCTTGATTGAGTTCTACTCTACTAACCACAAGAGCTCGGCGCCATTGCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT