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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttctattttataaagatattatttaaaattcatatggttggttttggaaaaagtagctttaggctgtgcttgtgcaacaatctaggattctat...

Basic information

species Zea mays
transcript GRMZM2G039345_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039345_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g56320.1 (Oryza sativa), 5'ss of exon 10
CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttctattttataaagatattatttaaaat-tcatatggttggttttggaaaaag---tagctttaggctgtgcttgtgcaacaatctaggattctat
|||||||||| |||||||||||||||||||||||||| |||| ||| |||||| |||||  | |  |  ||||  |     ||    |   | |  |   ||| ||||| ||||||    |  | | |   | ||  |||| |||||| |    |     
CTCTGGACTTTTATGGAGCTTTGAGATCCAGGACATACGATCGGGCAATCTTGCAGgtacctgtgttgatttaggacagagttcgcaattctattttccagttcgttttagaaaaaaaattcacctgattttttgtatgtgaaacaatgtcatgtc----
















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|13558638|gb|BG549994.1|BG549994
EST:     ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|94472576|gb|EB701534.1|EB701534
EST:     ACTTTTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|32800943|gb|CD953179.1|CD953179
EST:     GATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTA
genomic: GATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTA
EST: gi|13558280|gb|BG549636.1|BG549636
EST:     ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|149110162|gb|EE293978.2|EE293978
EST:     ACTTTTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|10450869|gb|BE924793.1|BE924793
EST:     ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|50339743|gb|CO534869.1|CO534869
EST:     ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|13558281|gb|BG549637.1|BG549637
EST:     ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
EST: gi|50324671|gb|CO519797.1|CO519797
EST:     ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGATATCTTGGAG                         TGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG
genomic: ACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAG

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), 43 (downstream exon)
Score: 57

CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAGCGAAAGAAAGGCGAGGAGCTTCCAACGTTTATACCCCCAAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 46

CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAGCGAAAGAAAGGCGAGGAGCTTCCAACGTTTATACCCCCAAAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 15

CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAGCGAAAGAAAGGCGAGGAGCTTCCAACGTTTATACCCCCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 69

CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttc ... tgcactgcagTGGGTCGAAGAAATCGGTGGGCATGAACAGCTAAATGAGAAGCTTCTTAAGCGAAAGAAAGGCGAGGAGCTTCCAACGTTTATACCCCCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGACTTCTATGGAGCTTTGAGATCCAGGACATATGATCAGGCTATCTTGGAGgtattttttctattttataaagatattatttaaaattcatatggttggttttggaaaaagtagctttaggctgtgcttgtgcaacaatctaggattctat

- - - - - - - GGAGCT
- - - - - - -  GAGCTT
- - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaag