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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaataaacattgcatcttttatcattgacatgtaactgagggtttccttatccatatgaatctcattttgacatgtgacatttcag

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 12
GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaataaacattgcatcttttatcattgacatgtaactgagggtttccttatccatatgaatctcattttgacatgtgaca--tttcag
|||||||||  | || ||||| ||| ||||||||||| | |||||||||||  |||| || |||||||| ||||||||||||||||| || ||||||||||||||||| |||| ||  | | | |||  ||||   | |   |   |  |  | ||| |   |  ||  |  |||| || |   ||||||
GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCTgtatggaataaccatttcaaatatcaccataaacataccaatctagaagttatcgtgcatgt---ttacaactaaacatctgccttctttcag
















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|60358486|gb|DN225459.1|DN225459
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|32937713|gb|CF042532.1|CF042532
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|211091998|gb|FL476411.1|FL476411
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|60351022|gb|DN217995.1|DN217995
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|19058677|gb|BM737344.1|BM737344
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAAC
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAAC
EST: gi|16918483|gb|BM073768.1|BM073768
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|60358733|gb|DN225706.1|DN225706
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|211167201|gb|FL456897.1|FL456897
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTAGGATCTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|22490645|gb|BU050568.1|BU050568
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|24769868|gb|CA404997.1|CA404997
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|5740120|gb|AI947810.1|AI947810
EST:     CCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: CCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|211126137|gb|FL125779.1|FL125779
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTAGGATCTCTATTGGAGCTAACATGGAACGGGCAGAA
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAA
EST: gi|94474487|gb|EB703445.1|EB703445
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|149008950|gb|EE153723.2|EE153723
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|5686716|gb|AI939809.1|AI939809
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|5740098|gb|AI947788.1|AI947788
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|149090119|gb|EE179417.2|EE179417
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT                         GAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG
genomic: GCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAG

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), 48 (downstream exon)
Score: 327

GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 302

GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 258

GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaata ... gacatttcagGAACCGGACTCCCTCGGATGTCTATTGGAGCTAACATGGAACGGGCAGAAGGAGATACCAGTGGGCAATTTGACCCGCAAGTTTCTAGAAGATGGAGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCTgtatggaataaacattgcatcttttatcattgacatgtaactgagggtttccttatccatatgaatctcattttgacatgtgacatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA