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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttctccctcattgatgatactagacatgcttttcttggttttctgatggtcagtgttgtcacccag

Basic information

species Zea mays
transcript GRMZM5G866758_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 7
GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttctccct--cattgatgatact-agacatgcttttcttggttttc--tgatggtcagtgttgtcacccag-----------------------
||||| | |||||| |||||||| ||||||||||||||||||||  |||||||||||||||||||||||||| ||||||| |||| ||  ||  || | ||  |  | |   ||   |  |    |  ||  | ||||  |  | | |||   |                        
GATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCGgtgatttcctgtctgccactaattttttttatttattactaaccaaatgctcattaatggcaacagatttcatataaatttaccacaattttgaatttta
















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|20300202|gb|BQ163145.1|BQ163145
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCA-CATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|31909501|gb|CD650950.1|CD650950
EST:     GTGG-GCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|18661821|gb|BM501596.1|BM501596
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|22490495|gb|BU050418.1|BU050418
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAA-CCCCC
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCC
EST: gi|18450558|gb|BM428836.1|BM428836
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|18654813|gb|BM499618.1|BM499618
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|87152006|gb|DY396795.1|DY396795
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|20300665|gb|BQ163608.1|BQ163608
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|211292808|gb|FL187022.1|FL187022
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|19821841|gb|BQ047865.1|BQ047865
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|22490486|gb|BU050409.1|BU050409
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCC
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCC
EST: gi|89106507|gb|DY576724.1|DY576724
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|18964777|gb|BM661218.1|BM661218
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTNGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|22490195|gb|BU050118.1|BU050118
EST:     GTGGAATTGCTGCTCG-GACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGAT
EST: gi|19770473|gb|BQ035194.1|BQ035194
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|20300437|gb|BQ163380.1|BQ163380
EST:     GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATT
EST: gi|19058058|gb|BM736725.1|BM736725
EST:     GTGGAATTGCTGCTCGTGACAATGGTGCTTTTGCATGGGAGATTATTCCG                         GTTCAAGTTCCTGTTGGTAGAGGAAAACCCCC
genomic: GTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCC

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: 160

GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttct ... tgtcacccagGTTCAAGTTCCTGTTGGTAGAGGAAAACCCCCAACATTAATTGAGAGAGATGAAAGCCTGGATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCGgtaattttctccctcattgatgatactagacatgcttttcttggttttctgatggtcagtgttgtcacccag

- - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT