Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaaaatttggctcttccataggcaactactattcacaaattgtagaagtgggatcttgattattgcatatatctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG

Basic information

species Zea mays
transcript GRMZM2G068244_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068244_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g60740.1 (Oryza sativa), 3'ss of exon 4
-----------gtaagctaaaatttggctcttccataggcaac--tactattcacaaattgtagaagtgggatcttgattattgcatatatctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG
           ||| | ||  || |  |   |  |    | ||  | ||  |  ||  || | | |      |    ||      || ||| || ||||||| |||||||||||  |||||||||||||||||||||||||| ||||||||||||| |||||
agtgccaaactgtatgatattatcttacaaatgaactttccacattgctgatatcaccttattggatattccttgatatggccttatttatttgttatagGTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG
















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|60397802|gb|DN230618.1|DN230618
EST:     GAACAAATCCTAACCATCCACTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32922742|gb|CF027554.1|CF027554
EST:     AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|20803051|gb|BQ294101.1|BQ294101
EST:     GAACAAATCCTAACCATCCACTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32922646|gb|CF027458.1|CF027458
EST:     AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|211113405|gb|FL349341.1|FL349341
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|116828080|gb|EC872039.1|EC872039
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGA
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGA
EST: gi|32922752|gb|CF027564.1|CF027564
EST:     AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32923432|gb|CF028244.1|CF028244
EST:     AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGACCAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32923376|gb|CF028188.1|CF028188
EST:     AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|60339573|gb|DN206546.1|DN206546
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|211283841|gb|FL366659.1|FL366659
EST:     GAACAAATCCTAACCATCCACTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|211537318|gb|FL320573.1|FL320573
EST:     GAACAAATCCTAACCATCCACTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|60343124|gb|DN210097.1|DN210097
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32923449|gb|CF028261.1|CF028261
EST:     AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGACCAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|211278086|gb|FL458575.1|FL458575
EST:     TAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: TAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|211193544|gb|FL459435.1|FL459435
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32911901|gb|CF016713.1|CF016713
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32844239|gb|CD983920.1|CD983920
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|60396304|gb|DN229173.1|DN229173
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|78023137|gb|DV491524.1|DV491524
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|32920219|gb|CF025031.1|CF025031
EST:     GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
genomic: GAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT
EST: gi|116825576|gb|EC869314.1|EC869314
EST:     AACAAATCCTAACCATCCACTGAACAGNCATGGGTAATGGCAATATACTG                         GTATGGAAGCGCAAAGCAGAACAGTATTTGGCAAACAGTGGAATCCCTTAT
genomic: AACAAATCCTAACCATCCGCTGAACAG-CATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTAT

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), 43 (downstream exon)
Score: 212

CTAAAGCTGCTGGAGTGAAGCATATTGTGCTGGTGGGATCTATGGGAGGAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 556

CTAAAGCTGCTGGAGTGAAGCATATTGTGCTGGTGGGATCTATGGGAGGAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 176

CTAAAGCTGCTGGAGTGAAGCATATTGTGCTGGTGGGATCTATGGGAGGAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 215

CTAAAGCTGCTGGAGTGAAGCATATTGTGCTGGTGGGATCTATGGGAGGAACAAATCCTAACCATCCGCTGAACAGCATGGGTAATGGCAATATACTGgtaagctaaa ... tctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactattcacaaattgtagaagtgggatcttgattattgcatatatctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG
                           tcttgat  putative branch site (score: 215)
                                attattgcatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctaaaatttggctcttccataggcaactactattcacaaattgtagaagtgggatcttgattattgcatatatctgctatagGTATGGAAGCGCAAAGCAGAACAGTATTTGGCAGACAGTGGAATCCCTTATACAATCATAAG

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