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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcgacccgtggcgtcgtcatttccctctccgattctcggctcattcattcgctgttttctcaccgggtgtgcctgctcctccggtgtctggcggtgtcggcggcag

Basic information

species Zea mays
transcript GRMZM2G020943_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020943_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g15820.1 (Oryza sativa), 5'ss of exon 2
GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcgacccgtggcgtcgtcatttccctctccgattctcggctcattcattcgctgttttctcaccgggtgtgcctgctcctccggtgtctggcggtgtcggcggcag
 | | | |  | || | ||||||| |||| ||||||| ||||  |||||||| ||||||||||||||| ||||||| | ||||||||||  |    |     | || || ||          | | || | || |   |  ||  || |  |      |   || | |  |  |  |   | ||| | |||||||||
AGGTGGTGACCGGGTTGCTGTCCAGCACGGCGTCGGCGGTGGTGAAGCAGCTCTGGTCGCTCAAATCGACCGCCACAAGGACGGgtaattcgtctgct----cctcctccttggagaaaagaaatttcagttcttgtgtgtgcgcttcttccggtttcttgaccggattatt-gacggtggtcggcggcggcggcag
















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|149005168|gb|EE039704.2|EE039704
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160636|gb|FL114499.1|FL114499
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|78114597|gb|DV532985.1|DV532985
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|76912974|gb|DV164954.1|DV164954
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211159050|gb|FL114492.1|FL114492
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160632|gb|FL114495.1|FL114495
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGG
EST: gi|31360064|gb|CD444421.1|CD444421
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|71764659|gb|DR962596.1|DR962596
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160637|gb|FL114500.1|FL114500
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160639|gb|FL114502.1|FL114502
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|149099000|gb|EE185013.2|EE185013
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|148958537|gb|EC904780.2|EC904780
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160642|gb|FL114505.1|FL114505
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160646|gb|FL114509.1|FL114509
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160635|gb|FL114498.1|FL114498
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|78118043|gb|DV536430.1|DV536430
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|89759931|gb|DY688587.1|DY688587
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160643|gb|FL114506.1|FL114506
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCNGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|74241599|gb|DT649513.1|DT649513
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211162232|gb|FL114510.1|FL114510
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|149076865|gb|EE165521.2|EE165521
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160633|gb|FL114496.1|FL114496
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160640|gb|FL114503.1|FL114503
EST:     GCAGTGGCCAAGCAGCTYGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GCAGTGGCCAAGCAGCT-GTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211159051|gb|FL114493.1|FL114493
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160644|gb|FL114507.1|FL114507
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|71325268|gb|DR799321.1|DR799321
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211162233|gb|FL114511.1|FL114511
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
EST: gi|211160638|gb|FL114501.1|FL114501
EST:     GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGG                         CGACGACGGCAGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG
genomic: GGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACG

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: 49 (upstream exon), 46 (downstream exon)
Score: 13

GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACGCGGTGGACACGGTGTTCGACGGCAGCAAGCTGGGGATCGAGCCGCACGC


Block sizes: 32 (upstream exon), 40 (downstream exon)
Score: 3

GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACGCGGTGGACACGGTGTTCGACGGCAGCAAGCTGGGGATCGAGCCGCACGC


Block sizes: 48 (upstream exon), 25 (downstream exon)
Score: 7

GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACGCGGTGGACACGGTGTTCGACGGCAGCAAGCTGGGGATCGAGCCGCACGC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 17

GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcg ... tcggcggcagCGACGACGGCCGTGACGGGGCGGTCCATGGTGAGGTACGAGGGCGGGTACGCGGTGGACACGGTGTTCGACGGCAGCAAGCTGGGGATCGAGCCGCACGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATTGCGGGCAGGCTCCTGTCCACCACGTCGTCGGCAGTGGCCAAGCAGCTGTGGTCGCTCAAATCGGCCGCCACCAAGACGGgtaatcggcgacccgtggcgtcgtcatttccctctccgattctcggctcattcattcgctgttttctcaccgggtgtgcctgctcctccggtgtctggcggtgtcggcggcag

- - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - -  CAGCTG