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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtgatggttgctttgctataaaccttcctaagattttttttgttacctaatggtattgtctgcttctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC

Basic information

species Zea mays
transcript GRMZM2G151916_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 3
gtacagtgatggttgctttgctataaaccttcctaagattttttttgttacctaatggtattgtctgcttctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC
||| | |  ||     | |   ||   ||| | | | | ||| |||||  | || |  |  | | |  ||   |||| ||||||||||| ||||||||||||||||||| || || ||||||||||| ||||||||||| ||||||||||||||| |||| || |||||||| |||||||
gtaaacttctg--cagtgtaacattgtcctcctttaaagtttatttgtctcttatt--tggtatttcttttatcattcagGCAAAATGTTTGGAGACTGGTGAGACTGTCGCCATTAAGAAGGTTTTACAGGACAAGCGTTACAAGAACAGGGAGTTGCAGATTATGCGATCAATGGATC

upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 3
gtacagtgatggttgctttgctataaaccttcctaagattttttttgttacctaatggtattgtctgcttctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC
                  || |  ||||   | | |    || |  | || |   |  |  |||  |  |  || || |||| || || || || || || ||||| || || ||||||||||| || ||||||||| | ||||| ||| ||||||||||||| |||||     | || |
-----------------gtg-tgcaaactcgctttaatcattctaggctaacgtttcttcctgttgggcttcac-ttcagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCCATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gtacagtgatggttgctttgctataaaccttcctaagattttttttgttacctaatggtattgtctgcttctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC
                  || |  ||||   | | |    || |  | || |   |  |  |||  |  |  || ||||||| || || || || || || ||||| || |||||||||||||| || ||||||||| | ||||| ||| ||||||||||||| |||||     | || |
-----------------gtg-tgcaaactcgctttaatcattctaggctaacgtttcttcctgttgggcttcac-tttagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

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|50339419|gb|CO534545.1|CO534545
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211449760|gb|FL269008.1|FL269008
EST:     ACATGGCAGANAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211451889|gb|FL269015.1|FL269015
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211451885|gb|FL269011.1|FL269011
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211451891|gb|FL269017.1|FL269017
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211449756|gb|FL269004.1|FL269004
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|31363742|gb|CD448099.1|CD448099
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211451886|gb|FL269012.1|FL269012
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|29577163|gb|CB617275.1|CB617275
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|86470098|gb|DY236468.1|DY236468
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211449759|gb|FL269007.1|FL269007
EST:     ACATGGCAGAGAGAGT-GTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGA
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGA
EST: gi|50339420|gb|CO534546.1|CO534546
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|6865198|gb|AW360548.1|AW360548
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|19822262|gb|BQ048286.1|BQ048286
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211449757|gb|FL269005.1|FL269005
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211451888|gb|FL269014.1|FL269014
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
EST: gi|211449762|gb|FL269010.1|FL269010
EST:     ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAG                         GCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG
genomic: ACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 330

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 354

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 442

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 297

ACTATCAGCTACATGGCAGAGAGAGTTGTGGGAACTGGATCATTCGGAATCGTCTTCCAGgtacagtgat ... ctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccttcctaagattttttttgttacctaatggtattgtctgcttctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC
                        acctaat  putative branch site (score: 297)
                                      tctgcttct  putative PPT
        taagattttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtgatggttgctttgctataaaccttcctaagattttttttgttacctaatggtattgtctgcttctacatttagGCAAAATGTCTGGAGACTGGTGAGACTGTTGCTATCAAGAAGGTTTTGCAGGACAAGCGCTACAAGAACAGGGAGCTGCAAATCATGCGATCCATGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA