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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaatccgaagacttgtcatgcactaactcacctgatatttcttactaagctgttttcctttgtttatcatgaaattgcag

Basic information

species Zea mays
transcript GRMZM2G005848_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005848_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os12g07880.1 (Oryza sativa), 5'ss of exon 15
CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaatccgaagacttgtcatgcactaac--tcacctgatatttcttactaagctgttttcctttgtttatcatgaaattgcag
|||| | ||||  |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||| || || |||||||||||   | | | |     ||  |  ||||    |  |||  ||| ||  | |  | | ||  |||| | ||||  |||||||||
CAGAAGGCTGGCACCCTCATCTGAAAGACTTGTGTATGCACTGGTTCACCAGATTTTCCATGGGATCAAAGAGCATTTTCTTGTCACCACAGAGCTTAAGgtctccctg--cagtaaatcctgcactccttaacgagtatatgaagtttattgttta--tatcttgttttgctcatca--aaattgcag
















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|86470810|gb|DY237180.1|DY237180
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCCCCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTTTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|78089725|gb|DV518099.1|DV518099
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|74034811|gb|DT535302.1|DT535302
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|60348324|gb|DN215297.1|DN215297
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|18172478|gb|BM347866.1|BM347866
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|71762146|gb|DR960083.1|DR960083
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTTTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|6012352|gb|AW061708.1|AW061708
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|71771944|gb|DR969881.1|DR969881
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|37393835|gb|CF634184.1|CF634184
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTTTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
EST: gi|67021034|gb|CO449783.1|CO449783
EST:     AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAG                         TTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA
genomic: AGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTA

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), 48 (downstream exon)
Score: 86

CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTAAGACAAGACCTTGAGTCAGCTTTCGAAGAGGAACTTGATAGCATCTTTG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 27

CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTAAGACAAGACCTTGAGTCAGCTTTCGAAGAGGAACTTGATAGCATCTTTG


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 13

CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTAAGACAAGACCTTGAGTCAGCTTTCGAAGAGGAACTTGATAGCATCTTTG


Block sizes: 46 (upstream exon), 20 (downstream exon)
Score: 12

CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaa ... gaaattgcagTTCAATTGCTTTCTCCTCATGCCGATTGTTGACAAACTACCAGCACTTCTAAGACAAGACCTTGAGTCAGCTTTCGAAGAGGAACTTGATAGCATCTTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGACGCCTGGTTCCCTCATCTGAAAGGCTTGTTTATGCGCTGGTTCACCAGATTTTTCATGGAATCAAAGAGCATTTTCTTGTCACCACTGAACTGAAGgtctccctaatccgaagacttgtcatgcactaactcacctgatatttcttactaagctgttttcctttgtttatcatgaaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG