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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaaaaaataacagtgacgccttgaaacttagtatcatatctttttaattaatccttaataattctaccgggcaatgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG

Basic information

species Zea mays
transcript GRMZM2G108849_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108849_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g24550.4 (Oryza sativa), 3'ss of exon 11
gtaagttc----aaaaaataacagtgacgcct-tgaaacttagtatcatatctttttaattaatccttaataat-tctaccgggcaatgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG
|||||| |     ||| |||  |||        |||||  | | || || | | |||  | |    |||||||| | |    ||  || ||    ||||||| |||||||||||||||||||||| ||| |||||||||||||| || |  ||||||||||| ||||| ||||| ||||| |||||    ||||  |
gtaagtccttggcaaatatataagttcaataagtgaaatgttgcataatttgtattttttgagctattaataatgtttggtcggtgatactg-gtagGATGGGTACTTCAAGATCATAAGGGGCACAAACGAATGTGGCATCGAAGAAGATGTTGTTGCTGGTATGCCCTCGACGAAGAACATGGTGAGGAACTATG
















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|6020622|gb|AW065655.1|AW065655
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|67013050|gb|CO441799.1|CO441799
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAAATGAATGTGGCATCGAGGA
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAA-TGAATGTGGCATCGAGGA
EST: gi|33100201|gb|CF060161.1|CF060161
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|37383229|gb|CF628607.1|CF628607
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAT
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|32924024|gb|CF028836.1|CF028836
EST:     CTTCTGCCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|5922310|gb|AW055599.1|AW055599
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|60347914|gb|DN214887.1|DN214887
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGNATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|33103672|gb|CF063632.1|CF063632
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|6095470|gb|AW120137.1|AW120137
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|32941550|gb|CF046369.1|CF046369
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|5005885|gb|AI711947.1|AI711947
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|37385964|gb|CF630150.1|CF630150
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|37376423|gb|CF624736.1|CF624736
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|32941251|gb|CF046070.1|CF046070
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|24934282|gb|CA452500.1|CA452500
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|6022514|gb|AW067547.1|AW067547
EST:     GAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: GAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
EST: gi|5361062|gb|AI795677.1|AI795677
EST:     CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGAT                         GATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG
genomic: CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAG

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: 223

CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 850

CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1092

CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 278

CTTCTGGCAAATCAGTGGAATAGAGGCTGGGGCGATgtaagttcaa ... tgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatcatatctttttaattaatccttaataattctaccgggcaatgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG
      atatctttttaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcaaaaaataacagtgacgccttgaaacttagtatcatatctttttaattaatccttaataattctaccgggcaatgctttacagGATGGATACTTCAAGATCATAAGGGGCAAAAATGAATGTGGCATCGAGGAGGGCGTTGTTGCTGGAATGCCATCGACAAAGAATATGGTTCCAAACTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA