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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctaccgtcccaccaccaccccctcgcttcgtgcttcctcctgggtctaatttccgcagcgctttgctctgtttggtcgagcgttccggctgacggagggtttttttttttggtttggatgcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG

Basic information

species Zea mays
transcript GRMZM2G004696_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004696_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g08320.1 (Oryza sativa), 3'ss of exon 2
gtcagtgctaccgtcccaccaccaccccctcgcttcgtgcttcctcctgggtctaatttccgcagcgctttgctctgtttggtcgagcgttccggctgacggagggtttttttttttggtttggatgcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG
                                               |  |      |||  || |   |  |||  |      ||   |   || ||   |||   ||        |    |         |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||||||
----------------------------------------------gtaagctcttcttcttcatcatct--ctcgatccatctgattctgttggttgttcgagcaatt--------gacgggaggaaagttgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTGCCGACGTACGAGGACAAGGACGGCGACTGGATGCTCGTCGG
















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|28986332|gb|CB351083.1|CB351083
EST:     CTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|161591654|gb|EY960089.1|EY960089
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGT
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGT
EST: gi|31612277|gb|CD568899.1|CD568899
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGATCTTCTCCCACTTCACCATCA                         GGAAAGT-CGCCGACGACCAGAAGAAGCTGGTGGACG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAA-GTTCGCCGACGACGAGAGGAAGCTGGTGGACG
EST: gi|18173156|gb|BM348544.1|BM348544
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|18162902|gb|BM332741.1|BM332741
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|31612276|gb|CD568898.1|CD568898
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|15632305|gb|BI679398.1|BI679398
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|18163244|gb|BM333083.1|BM333083
EST:     CTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGATGGTGGACGCGGTGAACGGGACGG
genomic: CTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|31362759|gb|CD447116.1|CD447116
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|211380527|gb|FL436057.1|FL436057
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|56382192|gb|CV984861.1|CV984861
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|78105144|gb|DV523562.1|DV523562
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|18175256|gb|BM350636.1|BM350636
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|211380526|gb|FL436056.1|FL436056
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|18163782|gb|BM333621.1|BM333621
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG
EST: gi|18168464|gb|BM338304.1|BM338304
EST:     CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCA                         GGAAGTTCGCCGACGACGAGAGGAAGCTGGTGAACGCGGTGAACGGGACGG
genomic: CCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGG

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: 45 (upstream exon), 49 (downstream exon)
Score: 84

GGCGCGCCCTACCTGCGGAAGGTGGACCTGCAGGCGTACGCCGGCTACGACCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GGCGCGCCCTACCTGCGGAAGGTGGACCTGCAGGCGTACGCCGGCTACGACCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GGCGCGCCCTACCTGCGGAAGGTGGACCTGCAGGCGTACGCCGGCTACGACCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GGCGCGCCCTACCTGCGGAAGGTGGACCTGCAGGCGTACGCCGGCTACGACCAGCTGCTCCGCGCGCTCCAGGACAAGTTCTTCTCCCACTTCACCATCAgtcagtgcta ... gcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgagcgttccggctgacggagggtttttttttttggtttggatgcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG
            ggctgac  putative branch site (score: 169)
                         tttttttttttggttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgctaccgtcccaccaccaccccctcgcttcgtgcttcctcctgggtctaatttccgcagcgctttgctctgtttggtcgagcgttccggctgacggagggtttttttttttggtttggatgcgcgcgcagGGAAGTTCGCCGACGACGAGAGGAAGCTGGTGGACGCGGTGAACGGGACGGAGTACGTACCCACGTACGAGGACAAGGATGGCGACTGGATGCTCGTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG