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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggcttgttctgtacgttcaaacctgctgctttctgtctttgatctcggttggtgcaaactagaactgcctgccagtagaatacatggaaaaatat...

Basic information

species Zea mays
transcript GRMZM2G174990_T03
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174990_T03 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 12
GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggcttgttctgtacgttcaaacctgctgctttct-gtctttgatctcggttggt--gcaaactagaactgcctgcc---agtagaatacatggaaaaatat--------------------------------------------------
 |||||||| ||||||||||| ||||| ||||||||  |||| || |||||||||||||| ||||| ||  | ||||||||| | ||||| || |||||||||  |||||||| ||     ||||    |   |||| |   |||   |||  ||   |  |||   | | |    ||        |    || ||| ||||||||                                                  
AACGAAGCCATCCGAGATGCCATTTGAAAAGGAGGAATTGCTGAATGCAGCCGTCCGCCGTGTGGATGCATTAGAAGCCGAGTTAATCTCTACAAAGAAGgta--ggcttgttttgc----tcaagatggtacctttttcagcttcattctgagtgaattggcagcttggcataaactatattggtttaggtatatgtaaaaatattactaccttataaaaagaaggtgatgaagtacttcaattttcatgagcag
















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|211055318|gb|FL438696.1|FL438696
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTCTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|16380026|gb|BI993269.1|BI993269
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|211483107|gb|FK977834.1|FK977834
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTCTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|31997891|gb|CD661822.1|CD661822
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|31611996|gb|CD568618.1|CD568618
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|71426246|gb|DR807296.1|DR807296
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTTTACGATGCTTTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|60672515|gb|DN475220.1|DN475220
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTCTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|60336722|gb|DN203695.1|DN203695
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTCTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
EST: gi|60336887|gb|DN203860.1|DN203860
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCCTCTACGATGCTCTGATGCGACAGGATGAGCTGCTGGCGTACATTGA
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTT-TACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGA
EST: gi|13557670|gb|BG549026.1|BG549026
EST:     CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAG                         GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC
genomic: CCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGAC

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: 44

GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 315

GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggctt ... ccgtgagcagGCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGAAGCCGTCCGAGATGCCGTTTGAGAAGGAGGAGCTGCTCAACGCAGCCGTCCGCCGCGTGGACGCGCTGGAAGCCGAGCTGATCTCCACGAAGAAGgtacgggcttgttctgtacgttcaaacctgctgctttctgtctttgatctcggttggtgcaaactagaactgcctgccagtagaatacatggaaaaatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaata