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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttcttattacaactctttatgggtgcctaaaggactactagttccttacagataccctgacaataaggggaatgttctgtttgaatag

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g35400.4 (Oryza sativa), 5'ss of exon 8
CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttt----tcttattacaactctttatgggtgcctaaaggactacta-gttcc----ttacagataccctgacaataaggggaatgttctgtttgaatag
| || |||||||| |||||| |  |||| ||  |||||   ||||||||    || || || || ||||||||||||||||| ||||||||||||||| || |    || ||||      |||  |    ||| |||    ||||   || |    | | || |    | ||||   |     | || | |  |     
CAATAGTTAGTTTTGGAGATGTGACAAGTGAACTGAAAAGAGAAGCTGAACAGTTAGGAGTATCTTGCTTTTCTTGGGAAGAATTTTCTTCAATGgttagtctgaattcctattttgctacttattccaagccaaaatatttacttcattacaggatcataggtgtttttacaagtggtaagttattttctcag-----
















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|148958443|gb|EC904677.2|EC904677
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211174084|gb|FL129199.1|FL129199
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211345429|gb|FL132812.1|FL132812
EST:     TGAGAGATTGGGCGTCTCCTGCTTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTTCCCATTAAA
genomic: TGAGAGATTGGGCGTCTCCTGCTTTT-CTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTT-CCCAATAAA
EST: gi|149076511|gb|EE165137.2|EE165137
EST:     TGAGAGATTGGGCGTCTCCCTGCTTTTCTTGGAAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACC
genomic: TGAGAGATTGGGCGTCTCC-TGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACC
EST: gi|87157287|gb|DY402076.1|DY402076
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGGAAAACA-GACTACCAACTTCCCA-TAAACGTAAGGAAGATATCTGTAC
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGG-AAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTAC
EST: gi|149086279|gb|EE175820.2|EE175820
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|149107582|gb|EE189463.2|EE189463
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCCATAAACGTAAGGAAGATATCTGTA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTA
EST: gi|71430909|gb|DR811959.1|DR811959
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTATC
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTA-C
EST: gi|93282461|gb|EB674725.1|EB674725
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|149085816|gb|EE175338.2|EE175338
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|148970227|gb|EE021164.2|EE021164
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211174082|gb|FL129197.1|FL129197
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211174078|gb|FL129193.1|FL129193
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211175750|gb|FL129201.1|FL129201
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTAC
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAA-CAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTAC
EST: gi|148999540|gb|EE036511.2|EE036511
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211399266|gb|FL448654.1|FL448654
EST:     CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: CTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
EST: gi|211175754|gb|FL129205.1|FL129205
EST:     TGAGAGATTGGGCGTCTCCTGCTTTTNCTTGGGAAGAGTTTTCTTCAATG                         GGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA
genomic: TGAGAGATTGGGCGTCTCCTGCTTTT-CTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACA

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: 49 (upstream exon), 49 (downstream exon)
Score: 282

CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACAATCATGTATACCAGCGGAACAACTGGAGATCCCAAAGGTGTGATAATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACAATCATGTATACCAGCGGAACAACTGGAGATCCCAAAGGTGTGATAATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 432

CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttc ... gtttgaatagGGAAAACAAGACTACCAACTTCCCAATAAACGTAAGGAAGATATCTGTACAATCATGTATACCAGCGGAACAACTGGAGATCCCAAAGGTGTGATAATCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATGgttcgttttcttattacaactctttatgggtgcctaaaggactactagttccttacagataccctgacaataaggggaatgttctgtttgaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA