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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgtttggctcttacgaaaggacatctaactgagttggttaggtagtctgaatagcactccttaggtcatgagtttaactctccgtgagaggga...

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 5'ss of exon 13
GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgtttggctcttacgaaa-ggacatctaactgagttggttaggtagtctga-atagcactccttaggtcatga-gtttaactctccgtgagaggga
|| ||||||||||||||||||||||||| |||||| ||||||||||| || |||||||||| | ||   || | |  |     || || |      |    |    ||| ||| || |  |   |     | | | | | || |   |   ||     
GTGTTGAAAGGCCACATTGCACTAGACACTGCTGTATTTCCTAATGGAACCACAGgtgagtattttgaactttcataattcatacttccatacatatgaactctagagtttgacattgatcatgtcgtaccctaatgataaaatggtctccaggt---

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 5'ss of exon 14
GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgtttggctcttacgaaaggacatctaactgagttggttaggtagtctgaatagcactccttaggt--catga-gtttaactctccgtgagaggga---
|||||||||||||| ||||||||||||| |||||| ||||| ||||| ||||||||||||| | ||  ||| | |       || |||| ||   |    |  | ||  | ||||    || |  | |  | | | | | || |    |  |||   |   
GTTTTGAAAGGCCATATTGCACTAGACAGTGCTGTATTTCCCAATGGAACGACAGgtgagtgttttgagctttcat------acttctatctatatgaactcaggagatttaatattgatcatgtgttaccctaatgataaaatggatgccagatttacca

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 5'ss of exon 12
GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtt--tgtttggctcttacgaaaggacatctaactgagttggttaggtagtctgaatagcactccttaggtcatgagtttaactctccgtgagaggga--
||||||||||||||||||||||| |||| |||||| ||||| ||||| || ||||||||||   ||||| |  |||    |    ||||||  |||  |    |||   | | || |    || |  |  |    | | || |  | |  ||| | |  
GTTTTGAAAGGCCACATTGCACTGGACACTGCTGTATTTCCCAATGGAACCACAGgtgagtgagtgttttgagcttttatacttccatctatatgaact---caggagattt-aacattgatcatgtgtcccaatgataaaatagctgccagatgtacc

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|50323429|gb|CO518555.1|CO518555
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211089695|gb|FL030414.1|FL030414
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211089690|gb|FL030409.1|FL030409
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|71439289|gb|DR820339.1|DR820339
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|67010801|gb|CO439550.1|CO439550
EST:     GCTGTGTTTCTCT-ATGGGACGACAG                         GACATGCTCTTGCTATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GCTGTGTTTC-CTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|13382055|gb|BG458730.1|BG458730
EST:     CCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: CCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211089692|gb|FL030411.1|FL030411
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211089696|gb|FL030415.1|FL030415
EST:     TTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: TTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|67018778|gb|CO447527.1|CO447527
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211089691|gb|FL030410.1|FL030410
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211089694|gb|FL030413.1|FL030413
EST:     TTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: TTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|32937410|gb|CF042229.1|CF042229
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
EST: gi|211092150|gb|FL030416.1|FL030416
EST:     GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAG                         GACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG
genomic: GAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTG

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: 229

GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgt ... aagtttgcagGACATGCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGAAAGGCCACATTGCACTAGACATTGCTGTGTTTCCTAATGGGACGACAGgtgagtttgtttggctcttacgaaaggacatctaactgagttggttaggtagtctgaatagcactccttaggtcatgagtttaactctccgtgagaggga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaggaca