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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgccgcgattctcatagggcgtcgcggcgcctcgtggcgtaggtctagatcgtttgcgtttgagtgtctcttgggttggtcccttgtgatttgtcttgtctgatttctgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC

Basic information

species Zea mays
transcript GRMZM2G071071_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071071_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 2
gtaatgccgcgattctcatagggcgtcgcggcgcctcgtggcgtagg-tctagatcgtttgcgtttgagtgtctcttgggttggtcccttgtgat-ttgtcttgtctgatttctg--tgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC
                                   |||||||||||| | | ||||| | |   | |   || || ||||  |||||  |||||| | || |||  || | | ||  |    ||| | ||||| || || || || |||||||| ||||||||||| |||||||| || || || |||||||||||||| |||||||||||||||||| | ||| 
---------------------------------gttcgtggcgtaggatttggatcggtcgtaatgggtggtttcatgggc-ggtccgatgtgatctcgtgttgcttgctgtttgcctatcacagTTAAAGGCACCTGTGATTGTCGTGGGGTGTAAGCTGGACCTTAGGGACGAGCAGCAGGTCAGCCTTGAGCAGGTGATGGCGCCCATCATGCAGACATTCA
















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|148971580|gb|EE022295.2|EE022295
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|149010209|gb|EE042027.2|EE042027
EST:     CGCCGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211370078|gb|FK987855.1|FK987855
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211370069|gb|FK987846.1|FK987846
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGAACTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|31355399|gb|CD439756.1|CD439756
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCTTATTTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|74244530|gb|DT652444.1|DT652444
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211370076|gb|FK987853.1|FK987853
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGC
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGC
EST: gi|211370077|gb|FK987854.1|FK987854
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCC-AGTTATCGTGGTGGGGTG
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTG
EST: gi|31353231|gb|CD437588.1|CD437588
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211367425|gb|FK987844.1|FK987844
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211367421|gb|FK987840.1|FK987840
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|148933977|gb|EC877975.2|EC877975
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211370074|gb|FK987851.1|FK987851
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAA
EST: gi|211370073|gb|FK987850.1|FK987850
EST:     CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAG                         CTGAAAGCCCCAGTT
genomic: CGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTT

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), 49 (downstream exon)
Score: 109

TCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

TCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 45

TCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

TCAGGCCGCCGATGCGGTCGTGCTCACCTACGCCTGCGACCGGCCCGCCACGCTGGAGCGGCTCAGTTCGTTCTGGCTTCCCGAGCTCCGGCGACTCCAGgtaatgccgc ... tgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtctcttgggttggtcccttgtgatttgtcttgtctgatttctgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC
                                   gtctgat  putative branch site (score: 101)
                                         tttctgt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgccgcgattctcatagggcgtcgcggcgcctcgtggcgtaggtctagatcgtttgcgtttgagtgtctcttgggttggtcccttgtgatttgtcttgtctgatttctgtgatgcagCTGAAGGCCCCAGTTATCGTGGTGGGGTGCAAGCTGGACCTGAGGGACGAACAACAAGTTAGCCTTGAGCAGGTTATGGCGCCCATCATGCAGTCCTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG