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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacatgctgtgctgccagtggctgccaagtaatgagttgagttgagcagagcggaggaactgcactgcactcacgacacgactcatccttgcgtttggcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAA

Basic information

species Zea mays
transcript GRMZM2G443985_T04
intron # 17
splice site 3'
intron type U2

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|78180091|gb|DV550464.1|DV550464
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTCGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|76288363|gb|DV027931.1|DV027931
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|74231924|gb|DT639838.1|DT639838
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|71439507|gb|DR820557.1|DR820557
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|78083294|gb|DV511687.1|DV511687
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|78109374|gb|DV527790.1|DV527790
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCG
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCG
EST: gi|76014684|gb|DT941854.1|DT941854
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|71418512|gb|DR804465.1|DR804465
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|89252818|gb|DY624604.1|DY624604
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|71771028|gb|DR968965.1|DR968965
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|50324042|gb|CO519168.1|CO519168
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|93016171|gb|EB641691.1|EB641691
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|78076561|gb|DV504995.1|DV504995
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|6973455|gb|AW438149.1|AW438149
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTCGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|148990681|gb|EE032078.2|EE032078
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|78084510|gb|DV512903.1|DV512903
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTNCA-G
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCT-CAAG
EST: gi|50337067|gb|CO532193.1|CO532193
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|91871743|gb|EB401700.1|EB401700
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|78109441|gb|DV527857.1|DV527857
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
EST: gi|93012122|gb|EB637642.1|EB637642
EST:     CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAG                         ATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA
genomic: CGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGA

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 49

CTCCGCAAGGGCTACAGGTTCGTCGCGGTCATGCCAGGCCAGTACTCGCTCGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 46

CTCCGCAAGGGCTACAGGTTCGTCGCGGTCATGCCAGGCCAGTACTCGCTCGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAA


Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 14

CTCCGCAAGGGCTACAGGTTCGTCGCGGTCATGCCAGGCCAGTACTCGCTCGACAAGCAGATCCTGCTGACATACATGGGCGCAGAGCTGTACGTAACAGgtatcacatg ... gcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggaactgcactgcactcacgacacgactcatccttgcgtttggcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAA
               cactcac  putative branch site (score: 14)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcacatgctgtgctgccagtggctgccaagtaatgagttgagttgagcagagcggaggaactgcactgcactcacgacacgactcatccttgcgtttggcaagcgcagATCCATCCCTGGGGTTCCCGGGCATAACCGCCAAGGTCGAGGAGCTCAAGAAGGAGCTGCCCAACGTGCACGTCCTCGACCAGTTCTCCAACAGAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC