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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatgtatcaaacgtctggacattgctgatggaactcttgtagtagttcagcacataccattctttttcctaatttgtgtttttgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT

Basic information

species Zea mays
transcript GRMZM5G856738_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G856738_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g43410.1 (Oryza sativa), 3'ss of exon 5
----aaacatgt-atcaaacgtctggacattgctgatggaactcttgtagtagttc-agcacataccattctttttcctaatttgtgtttttgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT
    ||  || | |  |   | | | |   ||   |   |||| || | || |||| ||||||| ||||  | |        || | |  ||| |  |   ||||||||||||||||||||||||| |||||||| || || |||||||||||||| ||||||||  |||| |||||||||||||||||||  ||||| ||||| |
atggaagaatttgagtatttggcagtagcatgtatacacaactgttctggtggttccagcacatgccatcatatca------ttatttccttgttttcccaaacagGCTGATGTTGATGGAAATGGAACCATTGACTATGCTGAGTTCATATCAGCGACAATGCACATGAACAGATTGGAGAAGGAAGACCACATACTTAAAGCAT

upper sequence: GRMZM5G856738_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G37260.1 (Glycine max), 3'ss of exon 5
aaacatgtatcaaacgtctggacattgctgatggaactcttgtagtagttcagcacataccattctttttcctaatttgtgtttt-----tgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT
    ||   |    |  |  || ||||    |   |   ||  | |  || |    | | |||  | |||| |||  | | |  |     | ||    |   ||||||||||| ||||||||||| ||||||||||||   || || ||| | || || |||||  |||||||| |||| |  || || |   ||   ||||| |
----atccttatggctacatgatattgtgattactaggtttccacttattgatttta-atcatggtctttcataaactatatgatgacaattatttggttctcagGCTGATGTAGATGGAAATGGAACCATTGATTACATTGAATTTATAACTGCTACCATGCACATGAATAGAATGGAAAGAGAGGATCACCTATATAAAGCCT

upper sequence: GRMZM5G856738_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G23650.1 (Arabidopsis thaliana), 3'ss of exon 6
aaacatgtatcaaacgtctggacattgctgatggaactcttgtagtagttcagcacataccattctttttcctaat--ttgtgtt--tttgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT
                                | || |||  |   | | ||  || |     ||       ||||  || || |  |||| | |  |    |||||||| | |||||| ||||  | |||||||||  |||||| |||||||||||||||||| |||| ||| | ||    || || |   |   ||  || |
--------------------------------gtaagtct-atcacaatccactactttgatgtcaaagcaataatgcttatgatgctttgtttcttt---tagGCTGATATGGATGGAGATGGATCAATTGATTACTTGGAGTTTATATCAGCCACAATGCATATGAACAGAATCGAACGTGAGGATCACTTGTACACCGCAT

upper sequence: GRMZM5G856738_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g00690.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------aaacatgtatcaaacgtctg--gacattgctgatggaactcttgtagtagttca-gcacat-accattctttttcctaatttgtgttt-----------------ttgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT
                                            |  | || |    |  |||   |    |||||   ||  | ||  | | |||    ||| | | |||| |  |      |   ||  |                 ||| | || |   ||||||||||| ||||||||||| || |||||||||   ||||| |||||||||||||||||| |||||||| |||| |  || ||||   ||   |  ||||
gtattttctcctctcttatgtatttgctatgtgaatgtgtttgtattcttgcagttgatttcttctgtggctgctgccagatatgttacacttgtttgtacaccttagcattttgatgatctgtccatggctcaagtaaaataacaagattggttcctttttcagGCTGATGTGGATGGAAATGGAACAATTGATTACATCGAGTTTATATCAGCCACAATGCATATGAATAGAATGGAAAGAGAGGACCACTTATATAGGGCTT

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|148934744|gb|EC878792.2|EC878792
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|211301856|gb|FL439770.1|FL439770
EST:     AATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGRAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|32930571|gb|CF035383.1|CF035383
EST:     AACCTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTA
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTA
EST: gi|94476938|gb|EB705896.1|EB705896
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|148950492|gb|EC896063.2|EC896063
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|71769639|gb|DR967576.1|DR967576
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|6952611|gb|AW424679.1|AW424679
EST:     ACCTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|78181002|gb|DV551375.1|DV551375
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|71311882|gb|DR792411.1|DR792411
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|50331248|gb|CO526374.1|CO526374
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|32828133|gb|CD967811.1|CD967811
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|32828205|gb|CD967883.1|CD967883
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
EST: gi|32825421|gb|CD965143.1|CD965143
EST:     AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCG                         GCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC
genomic: AACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCC

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: 46 (upstream exon), 48 (downstream exon)
Score: 165

TGATAACAGTGGGACAATTACTCTTGAAGAGCTAAGATCTGGTTTACCAAAACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 310

TGATAACAGTGGGACAATTACTCTTGAAGAGCTAAGATCTGGTTTACCAAAACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 413

TGATAACAGTGGGACAATTACTCTTGAAGAGCTAAGATCTGGTTTACCAAAACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 217

TGATAACAGTGGGACAATTACTCTTGAAGAGCTAAGATCTGGTTTACCAAAACTTGGTACTAAAATTTCTGAATCAGAAATCAAACAGTTGATGGAGGCGgtatgttcag ... ccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttcagcacataccattctttttcctaatttgtgtttttgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT
                           taatttgtgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatgtatcaaacgtctggacattgctgatggaactcttgtagtagttcagcacataccattctttttcctaatttgtgtttttgatcccatgaacagGCTGATGTTGATGGAAATGGTACCATTGATTACGCGGAGTTCATATCAGCCACAATGCATTTGAATAGATTGGAGAAGGAAGACCGTATACTCAAAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- -catgtat
- - - - - - - - -ctggaca
- - - - - - - - - - - - - gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - ttcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgttt