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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaacgcattgtttccgttgctttgcgtttctactgatttcacaaatcctttttttgtgatctgtaatgtgtattatgtgctcattgtgcag

Basic information

species Zea mays
transcript GRMZM2G018508_T01
intron # 28
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018508_T02 (Zea mays), 5'ss of exon 27
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 5'ss of exon 32
AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagc--taacgcattgtttccgttgct--ttgcgtttcta---ctgatttcacaaatccttttt----ttgtgatctgtaatgtgtattatgtgctcattgtgcag---------------------------------
 ||||||||||||||||||||||||| |||||||||||||| ||||||||||| |||||||| ||| ||||||    |||||||||||| |  |  |  |||  | | | || |  | |  | |||    ||  ||  ||||| ||         |||| | ||   |     | ||| |  |   |||                                     
CGAAACATGTATGGAGCTTGGGAGCAATATCTTGGACTGGAGCATCCAGACACGGCTCCTAGAAAGACACACAACGCTAATCAGgtacatccttggcagattaatacggatggtcatgggatgtctgcccctagttggacaaacccgagagagaattgtaacctaccactacaactatttcttttctgtttctggaatgtttgctaattgcatgttcttcatgcag
















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|67020734|gb|CO449483.1|CO449483
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|4753524|gb|AI657434.1|AI657434
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|67016472|gb|CO445221.1|CO445221
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|6020900|gb|AW065828.1|AW065828
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|88751977|gb|DY536118.1|DY536118
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|40334440|gb|CK368510.1|CK368510
EST:     CAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: CAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|67015347|gb|CO444096.1|CO444096
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|37376055|gb|CF624526.1|CF624526
EST:     CAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: CAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|67015345|gb|CO444094.1|CO444094
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|50332269|gb|CO527395.1|CO527395
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|32857251|gb|CD996932.1|CD996932
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|5871166|gb|AW017637.1|AW017637
EST:     GACTGGAACATCCAGACCCAGCTCCTAGGAAGGCNCACACAATTAATCAG                         AATCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|32943477|gb|CF048296.1|CF048296
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
EST: gi|74238602|gb|DT646516.1|DT646516
EST:     GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG
genomic: GACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAG

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: 141

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAGAAATTTGAGCAATGAGCTGCCAAGCAAGGGCTAAAATTGCTGTCCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAGAAATTTGAGCAATGAGCTGCCAAGCAAGGGCTAAAATTGCTGTCCTGAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 56

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAGAAATTTGAGCAATGAGCTGCCAAGCAAGGGCTAAAATTGCTGTCCTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 108

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaa ... cattgtgcagAACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGATAGAAATTTGAGCAATGAGCTGCCAAGCAAGGGCTAAAATTGCTGTCCTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCAGACACAGCTCCTAGGAAGGCACACACAATTAATCAGgtacagctaacgcattgtttccgttgctttgcgtttctactgatttcacaaatcctttttttgtgatctgtaatgtgtattatgtgctcattgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC