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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaagggacagttcaatactgtaataatattctaatatgattttgtaaacatttaaaatgggaatgatcagttattttaatccatggtgatattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 3'ss of exon 6
----tcaaagggacagttcaatactgt-aataatattctaatatgattttgtaaacatttaaaatgggaatgatcagttattttaatccatggtgatattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG
    |      ||   |   ||   |  || |  | |      | |  |  |    ||||||||   | ||| | |||||||||||||||||   || |||  ||||||||||||| |||||||| ||| ||||||| || |||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||
actattttgtagaatatctgatggagcgaacagaaataatgagtaacgtgttgttaatttaaaa---ggatgctgagttattttaatccatgacaatgttc--agGTTCTCCAAATTTTGGAACTCTACCGAAGGATTTATGAAGAATTTTTAGCAGTTCCAGTTTCTAAAGGGAGGAAAAGTGAGATGGAAAAATTTGCTGGTG
















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|71332073|gb|DR802941.1|DR802941
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTACAGAAGGATATA
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATA
EST: gi|7031274|gb|AW461012.1|AW461012
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTACCGAAGGATATACGAAGAATTTTTAGCA
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA
EST: gi|60338824|gb|DN205797.1|DN205797
EST:     GAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA
genomic: GAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA
EST: gi|67027739|gb|CO456488.1|CO456488
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GGTCTCCAAATATTGGAACTGTNACCGA-GGATATACGAAGAATTTTTAGC
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGT-ACAGAAGGATATACGAAGAATTTTTAGC
EST: gi|31359187|gb|CD443544.1|CD443544
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATGGGAACTGTACCGAAGGATATACGAAGAATTTTTAGCA
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA
EST: gi|67020078|gb|CO448827.1|CO448827
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTACCGAAGGATATACGAAGAATTTTTAGCA
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA
EST: gi|67027210|gb|CO455959.1|CO455959
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTACCGAAGGATATACGAAGAATTTTTAGCA
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA
EST: gi|32929788|gb|CF034600.1|CF034600
EST:     GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTA
genomic: GGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTA
EST: gi|51871150|gb|CV126034.1|CV126034
EST:     ACTAAAGAAGAGGCAGATGAAGAG                         GTTCTCCAAATATTGGAACTGTACCGAAGGATATACGAAGAATTTTTAGCA
genomic: ACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 443

GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 468

GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 283

GAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAGgtagaagtac ... atattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaacatttaaaatgggaatgatcagttattttaatccatggtgatattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG
                              ttttaat  putative branch site (score: 283)
                                              tattctc  putative PPT
                      atcagttattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaagggacagttcaatactgtaataatattctaatatgattttgtaaacatttaaaatgggaatgatcagttattttaatccatggtgatattctcagGTTCTCCAAATATTGGAACTGTACAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atccatg