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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaagcaacggtatgtttcgtcattggtctacgacattcatagagatatgcctaacacacacagacacacacatacacattcattgtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA

Basic information

species Zea mays
transcript GRMZM2G095141_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095141_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g04020.1 (Oryza sativa), 3'ss of exon 8
gtaagcaaagcaacggtatgtttcgtcattggt----------ctacgacattcatagagatatgcctaacacacacagacacaca------catacacattcatt-gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA
||||||||    ||   |  |   | || ||            | |    | | | | | | |  |  ||||  || | |  | |       |  |||  | | || || |   ||| |||||||||||||||||||||| || ||||| || || ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| || |||||||
gtaagcaaccacacttcacatcctgccaatgccaatgaacaaaccatcttactgaaaaacagacacagaacaaccagaaatgctctgttggtctaacatttccttttgtattaccagCTGGGGATCAACATAGTGGACTCATCAGTGTCAGGACTGGGAGGCTGCCCATATGCAAAGGGCGCCACCGGCAATGTCGCGACGGAGGACGTTGTGTACA

upper sequence: GRMZM2G095141_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 8
gtaagcaaagcaacggtatgtttcgtcattg---gtctacga-----cattcatagagatatgcctaacacacacagacacacaca---------tacacattcatt-gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA
||||||||    ||   |  |   | || ||    |  || |     | | |  | | | |  |  || |||  |||| |  | |           |||  | | || || |   ||| |||||||||||||||||||||| || ||||| || || ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| || |||||||
gtaagcaaccacacttcacatcctgccaatgccaatgaacaaaccatcttactgaaaaacagacacaaaacaatcagaaatgctctgcttggcctaacatttccttttgtattaccagCTGGGGATCAACATAGTGGACTCATCAGTGTCAGGACTGGGAGGCTGCCCATATGCAAAGGGCGCCACCGGCAATGTCGCGACGGAGGACGTTGTGTACA

upper sequence: GRMZM2G095141_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G30880.1 (Glycine max), 3'ss of exon 7
--gtaagcaaagcaacggtatgtttcgtcattggtctacgacattcatagagatatgcctaacacacacagacacacacatacacattcattgtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA
   |  | |  ||   ||||              |  || ||  |  |     | |    |||| |  |  ||      | |     |||||   |    |||||||||||| || |||||| || || || || || |||||||| || || ||||||||||| || ||||| || || ||||| ||||||||||| ||||
atcttggtactgcc-tggtagaaagaactgagaattcacaactgttgtgtttgtttcagaaaca-attcctacttggttaaatctggtcatttattttatagATGGGGATCAGCACAGTGGATTCATCTGTTTCTGGTCTTGGAGGTTGTCCATATGCCAAGGGTGCAACTGGGAATGTAGCCACTGAGGATGTCGTTTACA

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|211088485|gb|FL432076.1|FL432076
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|71301050|gb|DR786554.1|DR786554
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|76016005|gb|DT943175.1|DT943175
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCTCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|76016845|gb|DT944015.1|DT944015
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|91872712|gb|EB402669.1|EB402669
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|211227159|gb|FL464265.1|FL464265
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|71318555|gb|DR796038.1|DR796038
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|148950048|gb|EC895580.2|EC895580
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|30306657|gb|CD001330.1|CD001330
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|31911304|gb|CD651858.1|CD651858
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|149072591|gb|EE157105.2|EE157105
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|211081279|gb|FL464186.1|FL464186
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|211184211|gb|FL472379.1|FL472379
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|161587654|gb|EY960381.1|EY960381
EST:     TCCACGATACGTATGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTG
EST: gi|110950579|gb|EE170731.1|EE170731
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|211139185|gb|FL464627.1|FL464627
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
EST: gi|5761976|gb|AI967024.1|AI967024
EST:     TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAA                         ATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG
genomic: TCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCG

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), 48 (downstream exon)
Score: 36

GCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACAAGATTGCCGTTCATTTCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

GCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACAAGATTGCCGTTCATTTCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119

GCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACAAGATTGCCGTTCATTTCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 142

GCTTCAAGCTGTCATGTCGTTTGTCCCGGTGGACAAGATTGCCGTTCATTTCCACGATACGTACGGGCAGGCCCTTGCCAACATCCTCGTCTCCCTTCAAgtaagcaaag ... gtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagagatatgcctaacacacacagacacacacatacacattcattgtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA
         gcctaac  putative branch site (score: 142)
                                           ttgtctc  putative PPT
                                      attcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaagcaacggtatgtttcgtcattggtctacgacattcatagagatatgcctaacacacacagacacacacatacacattcattgtctcgtcagATGGGGATCAACATAGTGGACTCGTCGGTGTCGGGCCTTGGAGGCTGCCCGTATGCCAAGGGCGCCACTGGCAACGTCGCCACGGAGGATGTCGTGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG