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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtagctcgctcttgcccactgtgagccgtgcttccttacggactacatagcactgtgaatttaacccgtggacaccacacgtgctttcgtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC

Basic information

species Zea mays
transcript GRMZM2G178415_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
gtcagtagct-cgctcttgcccactgtgag---ccgtgcttccttacggactacatag---cactgtgaatttaacccgtgga--caccacacgtgctttcgtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC
|| |||  || | |  |  |||  ||  |    | | |      |    |  |   ||    |    ||   | |  | || |    |  |   |  | | || |||||||||||| ||||| |||||||||||||| |||||||| |||   ||||||  ||| |||||||| || |  ||| |||| |||||| |||||||| ||||||
gtaagttactgcacaatctccctgtgctaaattcagagtaaaaatgtaaagcagtcaggttaagcaagagactgatgcatgaagctgctgctgttcttgtggtttgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC

upper sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
-gtcagtagctcgctcttgcccactgtgagccgtgcttccttacggactacatagcactgtgaatttaacccgtggacaccacacgtgctttcgtctgtt-cagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC
 |    |||   ||| |     |   |||    |   |    || ||| |   |         ||||     || |  |      ||| ||| ||   || |||||||| || || ||||||||||| || ||||| ||||||   || |||||||||||||||||  | |  |||   || |||||| |||||||| | | ||
tgatgctaga--gctgtaatgaatgttgaatttta--taaaaactgacaatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC
















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|6851580|gb|AW352590.1|AW352590
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGTAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|50334795|gb|CO529921.1|CO529921
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|60344011|gb|DN210984.1|DN210984
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|71766898|gb|DR964835.1|DR964835
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|67040711|gb|CO466966.1|CO466966
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|6012198|gb|AW061740.1|AW061740
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|148981457|gb|EE027656.2|EE027656
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|101387651|gb|EB815840.1|EB815840
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTATTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGGACGAAGAGAAGGTAAACGCGGAGCTGCG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGT-GGGACGAAGAGAAGGTAAACGCGGAGCTGCG
EST: gi|148974520|gb|EE025306.2|EE025306
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|91053893|gb|EB164311.1|EB164311
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|78092009|gb|DV520383.1|DV520383
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|60394477|gb|DN227347.1|DN227347
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|149082771|gb|EE171994.2|EE171994
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|211079581|gb|FL056327.1|FL056327
EST:     TACTGGCCAACTCTGGTGGCGTCRCAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGA
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGA
EST: gi|60343914|gb|DN210887.1|DN210887
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|71426411|gb|DR807461.1|DR807461
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|211375022|gb|FL430803.1|FL430803
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|50330055|gb|CO525181.1|CO525181
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|86470639|gb|DY237009.1|DY237009
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|5922337|gb|AW055626.1|AW055626
EST:     TNCTGGCCAACTCTGGTGGCGTC-CAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|148940230|gb|EC884999.2|EC884999
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|14243831|gb|BG841522.2|BG841522
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|74245082|gb|DT652996.1|DT652996
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|148934216|gb|EC878237.2|EC878237
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|78077525|gb|DV505959.1|DV505959
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGAGGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|71328973|gb|DR801176.1|DR801176
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|50325461|gb|CO520587.1|CO520587
EST:     AGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: AGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
EST: gi|211079579|gb|FL056325.1|FL056325
EST:     TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA                         AACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG
genomic: TACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGG

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: 30 (upstream exon), 20 (downstream exon)
Score: 1

ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC


Block sizes: 34 (upstream exon), 16 (downstream exon)
Score: 1

ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC


Block sizes: 39 (upstream exon), 11 (downstream exon)
Score: 1

ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC


Block sizes: 35 (upstream exon), 41 (downstream exon)
Score: 7

ATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAAgtcagtagct ... gtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatagcactgtgaatttaacccgtggacaccacacgtgctttcgtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC
               atttaac  putative branch site (score: 7)
                                        ctttcgtct  putative PPT
            tgaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtagctcgctcttgcccactgtgagccgtgcttccttacggactacatagcactgtgaatttaacccgtggacaccacacgtgctttcgtctgttcagAACATCCAGGGGTTCATGTGGGACGAAGAGAAGGTAAACGCGGAGCTGCGGACGTACATGACGCGCGCCTTCGGGGACGTGAAGCAGATGTGCCGGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG