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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctcttgtttttttaaggccaaatgacatggatttgctatattgggctacctctgatcattggcatttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG

Basic information

species Zea mays
transcript GRMZM2G098569_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 7
gtaatgctcttgtttttttaaggccaaatgac-atggatttgc-tat-attgggctacctctgatcattggcatttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
           ||   |||    |    ||    || ||||   ||| | ||| ||||| |   | ||  |  ||||   ||||||||| ||||||||||||| |||||||||||| || |||||||||
-----------gtaccttttcaccttgttggttgtgaatttatatattactggactaccgc-actaatacgagttttctcacagGATGATTATCTAGATTGTTATGGTGATCCTGAGTTTATTGGCAAG
















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|76293424|gb|DV032992.1|DV032992
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|9953883|gb|BE640466.1|BE640466
EST:     TCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|76293423|gb|DV032991.1|DV032991
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|78117581|gb|DV535968.1|DV535968
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|149100778|gb|EE186872.2|EE186872
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|60339232|gb|DN206205.1|DN206205
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|60359240|gb|DN226213.1|DN226213
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|60355012|gb|DN221985.1|DN221985
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|148951737|gb|EC897492.2|EC897492
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|60341646|gb|DN208619.1|DN208619
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|148964885|gb|EE015747.2|EE015747
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|71310909|gb|DR791757.1|DR791757
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|148964886|gb|EE015748.2|EE015748
EST:     TTGATGTAAAGA-CATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCTTTGGCAAGATCGGA
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAGATCGGA
EST: gi|101397216|gb|EB820532.1|EB820532
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
EST: gi|78117582|gb|DV535969.1|DV535969
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGAT
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGAT
EST: gi|60353036|gb|DN220009.1|DN220009
EST:     TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAG                         GATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
genomic: TTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG

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: 148

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 541

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 208

GTTGCATGTGCATTGCTGCTGGCTGGTGAGAACTTGGAAAACTTTGTTGATGTAAAGAACATTCTCGTTGAAATGGGAACATACTTTCAAGTTCAGgtaatgctct ... ttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgacatggatttgctatattgggctacctctgatcattggcatttttctacagGATGACTATCTAGATTGTTTTGGTGATCCTGAATTCATTGGCAAG
                             ctctgat  putative branch site (score: 208)
                                          catttttct  putative PPT
                                           atttttcta  TA-rich tract