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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacaccgttgtgccttggatatcacgtgttttctttttcacttagggctagtttgggaactccattttcccatggaatttctatttttccaaggga...

Basic information

species Zea mays
transcript GRMZM2G164175_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164175_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 5'ss of exon 7
---CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacaccgttgtgccttggatatcacgtgttttctttttcacttagggctagtttgggaactccattttcccatggaatttctatttttccaaggga-
   | |||||||||||||||||||| | ||||||||||||||| |||||||||| |||||||| |||   ||| ||||||||||||||||||| |||   ||||||| ||   ||||   |||  | ||| | | ||  ||   |    ||||  ||       | ||   || |     | | |||  ||||  |    | | 
GGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACATTGTATTATTTGAGTCTGAAGAAAGGCAT---CTCAAGTTGCTTCTGCACAATTCTTTTAGAGAGgtaaaaccatgttgaatcttaaa-atctcttcttccctcagtttaataggcatatgcatataccttttttctgtttggtagtttagatttcccttttgtaa

upper sequence: GRMZM2G164175_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 5'ss of exon 6
---CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacaccgttgtgccttggatatcacgtgttttcttt-ttcacttagggctagtttgggaactccattttcccatggaatttctatttttccaaggga
   |||||||||||||||||||||| | |||||||| |||||| ||||||| || |||||||| |||||   | |||||||||||| |||||| ||||  ||||||| |||| ||||   |||  | ||| | | ||  ||   |||| |  |     |  |         |   |       ||| | |  | ||  |     
GGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATTGTATTATTTGAATCTGAAGAAAGGCATGT---CAAGTTGCTTCTGCGCAATTCATTTCAAGAGgtaaaacactgttgaatcttaaaaatctcttcttccctcagttcaataggtatacgcatttatttagtagcctgtttataaatatatgatgttttagtaa-

upper sequence: GRMZM2G164175_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv11s0037g01100.t01 (Vitis vinifera), 5'ss of exon 10
CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacaccgttgtgccttggatatcacgtgttttctttttcacttagggctagtttgggaactccattttcccatggaatttctatttttccaaggga
 ||  ||     |||||  |||  |   |||||||||||||| ||||| ||||||||||||    |     | || ||  |     |||| ||    ||||||      | || |   |||  | |||     ||  ||||| |  |  |   | |||      | | |||     ||   ||  | |  || ||     
AGAATTTGCAATAAATTGGTCTCTACCTAGTCACATTGTAATGTTTGATTCAGAAGAAAGATCACTAAGGGAATTTCTAGTTTCACATTCTTTCAAAGAGgta------cattctagtttg--tttca-----ttagttttttaagtgag--caattttttcttttcttttgtggctgatcttgttgtaattgcag----

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|71427411|gb|DR808461.1|DR808461
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|71314140|gb|DR793687.1|DR793687
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|40336287|gb|CK370357.1|CK370357
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|71764471|gb|DR962408.1|DR962408
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|6654204|gb|AW267609.1|AW267609
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|88748600|gb|DY532741.1|DY532741
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|71321848|gb|DR797614.1|DR797614
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|76932561|gb|DV173073.1|DV173073
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|4826073|gb|AI667701.1|AI667701
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|211236953|gb|FK974486.1|FK974486
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|211236952|gb|FK974485.1|FK974485
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTTCCACTCACATTTTCAAGGTTGACAGAGACCTTCAGT
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTT-CCACTCACATTT-CAAGGTTGACAGAGACCTTCAGT
EST: gi|148948729|gb|EC898651.2|EC898651
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTTTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|37392942|gb|CF633725.1|CF633725
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
EST: gi|211131602|gb|FL458961.1|FL458961
EST:     CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAG                         ATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG
genomic: CAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCG

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), 48 (downstream exon)
Score: 85

CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCACGGAGGAATGTGCTCTGATTTAGTACTGATG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 27

CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCACGGAGGAATGTGCTCTGATTTAGTACTGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCACGGAGGAATGTGCTCTGATTTAGTACTGATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 56

CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacacc ... tggttggcagATGAGGAGGTTTTTCCACTCACATTTCAAGGTTGACAGAGACCTTCAGTCGGCTGTTGTGGTTTATTCACGGAGGAATGTGCTCTGATTTAGTACTGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATTGTAATATTTGAGTCAGAAGAAAGACATGTTCTCCAGTTGCTTCTGCACAATTCCTTTCTTGAGgtaacacaccgttgtgccttggatatcacgtgttttctttttcacttagggctagtttgggaactccattttcccatggaatttctatttttccaaggga

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA