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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccattaaacaggtgcagtatttcaggtgtttgtaaactgatatataaccaagtgtaatctttcttgtgcag

Basic information

species Zea mays
transcript GRMZM2G123709_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123709_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g39760.1 (Oryza sativa), 5'ss of exon 3
ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaag---ccattaaacaggtgcagtattt-caggtgtttgtaaactg--atatataac---caagtgtaatctttcttgtgcag------------------------
|||||| || || ||||| |||||||||||||| ||||| || |||||||| |||||||| |||||||| ||||| || || || ||  |||||||||||||| |   |||   | |   | |    ||  ||  || |  |   | |  || |||||    ||| || | |  ||  |||  |                         
ATTGCTAGGCGATCATGATGGAAGGGCTCACAAGTTGGCCATTGAGCCTGGCAGTCCTTATATTTTCTATAGCTGCGGCGAAGATGGGCTTGTTCAACATgtagggaaccacggaccccctccctccttcacaaatgctcattttcagctatgtataaaatgcaaatgaatttcttactgtataactagccacttcccttcttgtgcag

upper sequence: GRMZM2G123709_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G23960.1 (Glycine max), 5'ss of exon 3
ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccattaaacaggtgc--agtatttcaggtgttt-gtaaactgatatataaccaagtgtaatctttcttgtg-cag
 |  || |   | ||| | ||||||||||| || |||||||| ||||||||||| ||| | ||||| || | ||||||||| || || || || || | ||| || |||| |     | |  | | |||  | | |||  |  | || |      |  | |      |||||| || |||
GTGTCTGGCCAAGCATCAAGGAAGGGCTCATAAGTTGGCTATTGAGCCTGGTAGCCCTCATATTTTTTATACCTGTGGTGAAGATGGATTAGTGCAGCGTgtgagtcattcatttctttcctactttttttgttattttatttattgtttatcctctcactaagtgttttcttttgacag
















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|149074562|gb|EE162962.2|EE162962
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|28909535|gb|CB330979.1|CB330979
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAAC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAAC
EST: gi|6095576|gb|AW120243.1|AW120243
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|76924931|gb|DV170201.1|DV170201
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|76934227|gb|DV173775.1|DV173775
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|148996165|gb|EE035435.2|EE035435
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|76019007|gb|DT946177.1|DT946177
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|78111955|gb|DV530351.1|DV530351
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|148969559|gb|EE020388.2|EE020388
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|93014861|gb|EB640381.1|EB640381
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|149112432|gb|EE191333.2|EE191333
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|76017451|gb|DT944621.1|DT944621
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|148940255|gb|EC885028.2|EC885028
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|78105452|gb|DV523870.1|DV523870
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|78086093|gb|DV514486.1|DV514486
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
EST: gi|148949179|gb|EC894616.2|EC894616
EST:     GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACAT                         TTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC
genomic: GTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCC

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: 48 (upstream exon), 49 (downstream exon)
Score: 278

ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCCACTAAATCAGTATACTCATCTCTTGTTCACCTAAATGCGCTTGCAATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 159

ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCCACTAAATCAGTATACTCATCTCTTGTTCACCTAAATGCGCTTGCAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCCACTAAATCAGTATACTCATCTCTTGTTCACCTAAATGCGCTTGCAATAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 344

ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccatt ... tcttgtgcagTTTGATCTCAGAACAAACACAGCCTCAAAACTATTTCTTTGCAGAAACTCCACTAAATCAGTATACTCATCTCTTGTTCACCTAAATGCGCTTGCAATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTTGGTGAACATGAGGGAAGGGCTCACAATTTGGCTATAGAGCCTGGTAGTCCTTACATTTTCTACAGCTGTGGTGAGGAAGGCTTTGTTCAACATgtaagccattaaacaggtgcagtatttcaggtgtttgtaaactgatatataaccaagtgtaatctttcttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG