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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgttaagttcaagagctggttatgtcaggaatctgaatgaacatactcagtctaattgttcattgtgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG

Basic information

species Zea mays
transcript GRMZM2G116427_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116427_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g49890.1 (Oryza sativa), 3'ss of exon 4
gtcagtgttaagttcaagagctggttatgtcaggaatctgaatgaacatactcagtctaatt-----gttcat-----tgtgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG
||| || ||||    | ||| |  || |  ||| ||| ||||  | || |||  |||| |||     |||| |     ||||||||||||||||||||| ||||||||||| ||||| |||||  ||||||| || |||||||||||
gtcggtattaaacctatgagatttttgtaacagtaatgtgaactagcacacttggtctgattctcttgttcttcattttgtgtgaaacagGTATGAGATTGACAAGGTCACTGCAGGTCAGCGGCTGGATCTAAACCTTGAAAGAGG

upper sequence: GRMZM2G116427_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G24320.1 (Glycine max), 3'ss of exon 5
--------------------------gtcagtgttaagttcaagagctggttatgtcaggaatctgaatgaacatactcagtctaattgttcattgtgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG
                          |      | || | | | || ||  |   |  |   ||||     |  |     ||  |||      || |||||  |||||||||||| ||||| ||||| || || |||||||| ||| |||| |||||||| ||
gtatgctttatcagtttcaacaattggctttgatcaactactatagatgtattcatttgt--tctgttatgatttttatggttcaatcacatgttttgtgatgcagGTATGAGATAGACAAAGTCACTGCTGGGCAGCGATTAGATTTGAACCTTGAAAGGGG

upper sequence: GRMZM2G116427_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G51090.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtgttaagttcaagagctggttatgtcaggaatctgaatgaacatactcagtctaattgttcattgtgtgaa----acagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG
|||||        | |  | |   ||| ||   || |    ||  ||    |||||   | ||   || |    ||     |||  | |||||||| || ||||| |||||||| || ||||| ||||||||||||| |||
gtcagctcc---ctaataaacc--ttaagttttgatttgctatagactcgatcagttgcactgactatcgcaataacattgcagACACGAGATCGATAAAGTCACAGCAGGACAACGGTTGGACCTGAATCTTGAAAAAGG

upper sequence: GRMZM2G116427_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G16460.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtgttaa--gttcaagagctggttatgtcaggaatctgaatgaacatactcagtctaattgttcattgtgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG
||  |||   |  ||||     || || || |         ||||    | ||| || |  |       |    ||||||||||| || || || |||||||| || ||||| || |||||| ||||||||||||||||
gtttgtgaccatagttcgc---cttgtaatattcttttaacgaatctgaaaactaagacctaagacctctcacttgaaacagGTACGAAATTGATAAGGTCACAGCGGGACAACGCTTGGATTTGAATCTTGAAAGAGG

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|21330027|gb|BQ485408.1|BQ485408
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|32869175|gb|CF008857.1|CF008857
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAT                         TTTTGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|21390796|gb|BQ528845.1|BQ528845
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCTCCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|21480752|gb|BQ577435.1|BQ577435
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|14324103|gb|BG929580.1|BG929580
EST:     GATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|6851592|gb|AW352602.1|AW352602
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGNCAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|21390595|gb|BQ528644.1|BQ528644
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|21480787|gb|BQ577470.1|BQ577470
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|26455505|gb|CA827088.1|CA827088
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|5922394|gb|AW055683.1|AW055683
EST:     GATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGNCAAGGTCNCCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|22546799|gb|BU099110.1|BU099110
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|211128611|gb|FL432588.1|FL432588
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGAACAGCGATTGGATYTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|21481481|gb|BQ578164.1|BQ578164
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|87154790|gb|DY399579.1|DY399579
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|22546847|gb|BU099158.1|BU099158
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACANGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
EST: gi|32906186|gb|CF010999.1|CF010999
EST:     GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAA                         GTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA
genomic: GAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGA

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), 45 (downstream exon)
Score: 53

GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 71

GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 83

GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 89

GAAAACCATTTCTCTTTACTACAGCGGGAGACTGAGAAACTTCGCGGAGATATTGATAAGATGAGGAGTGAACTGAAgtcagtgtta ... tgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtcaggaatctgaatgaacatactcagtctaattgttcattgtgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG
                             gtctaat  putative branch site (score: 89)
                                taattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgttaagttcaagagctggttatgtcaggaatctgaatgaacatactcagtctaattgttcattgtgtgaaacagGTATGAGATCGACAAGGTCACCGCAGGACAGCGATTGGATCTGAATCTTGAAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG