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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaacgcaagtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggcactgactgtaaa...

Basic information

species Zea mays
transcript GRMZM2G112865_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g62210.1 (Oryza sativa), 5'ss of exon 3
GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgt---aattggaacgca------agtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggcactgactgtaaa
||||||||||| ||||| ||||||||||||||||||||||| ||||| |||||   || ||  ||         | ||||||| ||| |   || ||  ||| ||||| |     |  ||| |||  |||| |||| ||||| || ||  ||        
GCGAAGGAGGTGCGGCGCAAGGCGGATCAGATGGTGCAGCTCGGGAAAGAGgtaaaaactgctacctgtgaaacattctcctgttgccatagaactat-aacctgaaaaaaattactgtttagtgccatccatgaacctatgtagagctttg--------

upper sequence: GRMZM2G112865_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g38580.1 (Oryza sativa), 5'ss of exon 3
GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaacgcaagtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggc-actgactgtaaa-
||||||||||| |||  ||| |||||||||||||||||||| || || ||||||        |      |    |  | |  |  | |    | |    | | |  |  ||     | || ||  |  || ||| ||||    | | |||   
GCGAAGGAGGTGCGGACGAAAGCGGATCAGATGGTGCAGCTCGGCAAAGAGgtatacattctgtcgagatgaaaactcaagctggaaattctcgttct-tgtgcaactcttgttctgaattctc-atcctttgctgggccgtaggcggtagca
















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|32909297|gb|CF014109.1|CF014109
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|50337604|gb|CO532730.1|CO532730
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|110963515|gb|EE183415.1|EE183415
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|37393499|gb|CF634015.1|CF634015
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|211500584|gb|FL212575.1|FL212575
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|60353121|gb|DN220094.1|DN220094
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|60356193|gb|DN223166.1|DN223166
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|22490485|gb|BU050408.1|BU050408
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|21987795|gb|BQ779323.1|BQ779323
EST:     GGAT-AGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGG-GATGAT
genomic: GGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|60397912|gb|DN230728.1|DN230728
EST:     GGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: GGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|87151864|gb|DY396653.1|DY396653
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|18965108|gb|BM661397.1|BM661397
EST:     GGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: GGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|50337603|gb|CO532729.1|CO532729
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|19058032|gb|BM736699.1|BM736699
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
EST: gi|148963908|gb|EE015020.2|EE015020
EST:     CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAG                         GGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT
genomic: CGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGAT

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: 261

GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaa ... cgatatgtagGGTACTCAGCATGCAGCAAGACGTGCTGCTGCCTTTGTTCGGGGTGATGATGTCGTTCATAAGCTATTTACTGAGCTGGCCTTTCGCTACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAAGGAGGTTCGGCGGAAGGCGGATCAGATGGTGCAGCTAGGGAAGGAGgtaattggaacgcaagtctcctgatgctaattaaataccaacttgaaatatccggccatttcgtggtatccttgaatctatgcagggcactgactgtaaa

-  AAGGAG
- - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - -  AAGGAG