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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctcgcaccccccttacaagtgctttagtttgttttatctgtaaacatgtaatcatgccttgacaattcttgtgattgttgaaaatggtgcatt...

Basic information

species Zea mays
transcript GRMZM2G138505_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138505_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 5'ss of exon 3
GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctcgcaccccccttacaagtgctt--tagtttgttttatctgtaaacatgtaatca--tgccttgacaattcttgtgattgttgaaaatggtgcatt
|||||||| |  |||||||| || |||||||||||||| ||||||| ||||||||||||||| ||| | |||||||| || || ||||| ||||||||||||||      |||||||       || |||  | |||| |||| |   |  |  |  | |||  ||| | |  |  | || |||    | | ||  ||     
GGTCATGAGGATCGATATTCCATTTATATCCATGCATCGCGTGAAAGACCTGTACATTCTAGTTCTTTGTTTGTTGGCCGAGAGATTCATAGTGAAAAGgtactaatgttcacccccacactgtgtacttgtttgtttcttttcttgctttatcttaactcatctgcttagcaaggtgttatgaacaataagaaatgtt----
















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|213187878|gb|FM187980.1|FM187980
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
EST: gi|60398184|gb|DN231000.1|DN231000
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
EST: gi|149081143|gb|EE170252.2|EE170252
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
EST: gi|101387923|gb|EB815975.1|EB815975
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTT
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTT
EST: gi|78081340|gb|DV509752.1|DV509752
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
EST: gi|71772237|gb|DR970174.1|DR970174
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGNGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
EST: gi|31355242|gb|CD439599.1|CD439599
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA
EST: gi|71447439|gb|DR828489.1|DR828489
EST:     CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAG                         GTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGGTAGGA
genomic: CTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGA

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: 48 (upstream exon), 47 (downstream exon)
Score: 159

GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGAAATGCATTGGAAGATGTTGATAATCAATTTTTCGTCTTGCTTTCTGACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 136

GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGAAATGCATTGGAAGATGTTGATAATCAATTTTTCGTCTTGCTTTCTGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGAAATGCATTGGAAGATGTTGATAATCAATTTTTCGTCTTGCTTTCTGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 154

GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctc ... tgaactgcagGTAGTATGGGGGAGGATTTCAATGGTTGATGCAGAGAAGAGGCTGTTAGGAAATGCATTGGAAGATGTTGATAATCAATTTTTCGTCTTGCTTTCTGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCATGATGGCCGATATTCTATCTATATCCATGCATCTCGTGAAAAACCTGTACATTCTAGCTCTCTTTTTGTTGGGCGTGAAATTCACAGTGAAAAGgtactccctcgcaccccccttacaagtgctttagtttgttttatctgtaaacatgtaatcatgccttgacaattcttgtgattgttgaaaatggtgcatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccct