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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcatatattcagtactgcatctattgttatcatgttatctctccctgtgatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os10g10190.1 (Oryza sativa), 3'ss of exon 13
gtgagtttcatat--attcagtactgcatctattgttatcatgttatctctccctgt---gatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT
|||||||| || |  | | | | |||     |||   ||  |  | | | |  || |   |||||||||| |||  ||||||||||||| || |||||||||||||| || |||||||||||||||||||||||||| || ||| | || ||||| |||||| | |  |||||||| |||||
gtgagttttatgtttaattaatgctgtcatcattcacattttactttttttttctctctggatgacaattttcatgatttagGTGTACTGGAGGCAAATTTTATTGAGCCGGCACATGACAAACAAGATTTTGAGAGAACCCCACTATTCATTCGACTAGAAGCTAAGCTTAGACAGATTAT

upper sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA02G05800.1 (Glycine max), 3'ss of exon 15
---------------------------------------------------------------------------gtgagtttcatatattca-gtactgcatctattgttatcatgttatctctccctgtgatgacaattgtcaca-atttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT
                                                                             ||||    |||| ||   |||||||| |  |     ||   | || |    | | |     | ||  ||| ||||||| || |||||||| |||||||| |||||||| |||||||| || |||||||||||  ||    |||| |||||| | ||||  | ||| | |||||| | 
gtatatttttatttttcttcgctgttgcattttctctgcatagaagagtatacatcactctaagtaaaatatacttagagtaatgtatactcttatactgcatatccttactccaaaat-tcccaggtttttaaatttactggtacatatttagGGGTTCTTGAAGCCAATTTTATAGAACCAGCGCATGACAAGCAGGATTTTGAGAGATCAGTGCTGTTCATTCGGTTGGAAAACAAACTGAAACAAATGAC

upper sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv04s0023g02740.t01 (Vitis vinifera), 3'ss of exon 13
gtgagtttca---tatattcagtactg-catctattgttatcatgttatctctccctgtgatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT
||  ||||     || |||   |  |  ||   ||| |  | ||| | |         |      |||    |   |  ||| || |||||||| |||||||| |||||||| ||||||||||| |||||||||||  || |  ||||||| || || |||||||  || | ||||||  |
gtatgttttcctctacattttatgttctcaaacattttccttatgatctagtcatgcattgcttgaatgcatatgttgcagGAGTTCTTGAAGCTAATTTTATAGAACCAGCGCATGACAAACAGGATTTTGAGAGATCATCTCTGTTTATCCGTCTCGAAACAAAGCTGAAACAAATGCT

upper sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ29839 (Selaginella moellendorffii), 3'ss of exon 12
gtgagtttcatatattcagtactgcatctattgttatcatgttatctctccctgtgatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT
              |    ||||| ||  | | | || | |  ||  ||| ||      ||||||||     |  |||  | ||||| || || |||||||||||||| ||||| |||||||||||||||| |||    ||| |  | || || ||||  || || |  ||||| | 
-------------gtgtgttactg-atgaagt-tcataaagacattgctctctc-----acaattgtt----tccagGGATTCTTGAGGCCAACTTTATTGAACCAGCTCATGATAAACAAGATTTTGAGAAGACGTGTTTGCTGTTGCGCCTGGAAAACAGGCTGAAGCAAATGAC

upper sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ08242 (Selaginella moellendorffii), 3'ss of exon 12
gtgagtttcatatattcagtactgcatctattgttatcatgttatctctccctgtgatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT
              |    ||||| ||  | | | || | |  ||  ||| ||      ||||||||     |  |||  | ||||| || || |||||||||||||| ||||| |||||||||||||||| |||    ||| |  | || || ||||  || || |  ||||| | 
-------------gtgtgttactg-atgaagt-tcataaagacattgctctctc-----acaattgtt----tccagGGATTCTTGAGGCCAACTTTATTGAACCAGCTCATGATAAACAAGATTTTGAGAAGACTTGTTTGCTGTTGCGCCTGGAAAACAGGCTGAAGCAAATGAC

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|78022987|gb|DV491374.1|DV491374
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|89758497|gb|DY687658.1|DY687658
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|211404582|gb|FL228991.1|FL228991
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|211460682|gb|FL127584.1|FL127584
EST:     AGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: AGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|5915604|gb|AW053245.1|AW053245
EST:     TAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|5361116|gb|AI795731.1|AI795731
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|9794197|gb|BE552505.1|BE552505
EST:     TTTCTGTAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|211404583|gb|FL228992.1|FL228992
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|78106768|gb|DV525186.1|DV525186
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTG                         GTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: TTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG
EST: gi|12968788|gb|BG265825.1|BG265825
EST:     GAGAAGTGTGGTTG                         GTGTACTTGAAGCAAA-TTTATTGAACCAGCACATGACAAACAAGATTTTG
genomic: GAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTG

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: 125

CCTTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 86

CCTTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 73

CCTTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 86

CCTTTCTGGAAGGTCCTTCAAGAAGGATCTAGCAGAGGGAGAAGTGTGGTTGgtgagtttca ... cacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatctattgttatcatgttatctctccctgtgatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT
      tattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcatatattcagtactgcatctattgttatcatgttatctctccctgtgatgacaattgtcacaatttagGTGTACTTGAAGCAAATTTTATTGAACCAGCACATGACAAACAAGATTTTGAGAGGACACCATTGTTTATTCGGCTAGAAACAAGACTTAGACAAATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA