Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacttgttaacaatgtaattttgtttctgttatttgtatgatgttattgttcttctttattaccatttttattagttatccaacttttaactcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC

Basic information

species Zea mays
transcript GRMZM2G091265_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 3
--taacttgttaacaatgtaattttgtttctg-ttatttgtatgatgttattgttcttctttattaccatttttattagttatccaacttttaactcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC
  |  | ||  |   |||  |    |||||   ||   || |  || |      | || ||| ||    || |||||   ||| ||||||||||||  || ||||||||||| |||||||||||||||||||||||||| || |||||  ||||||||| | ||||| | |||||||  |||||||||||  | |||||||| 
gttgtcatgc-actcatgctacacagtttccaatttgctgcaccatttctccaattttttttcttgt--ttattattgaatattcaacttttaacttgtgcagGTTCCATCCATCTTGTATGGGAATGACCATTGAGCAGGCCAAAAAATTAGATCATTTCCTGTGCGCAGATTGTGTCAAAGAAAATGGCACGAAGAGACCT
















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|211292773|gb|FL412753.1|FL412753
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGG
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGG
EST: gi|9952858|gb|BE639441.1|BE639441
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|50325986|gb|CO521112.1|CO521112
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|148933222|gb|EC876874.2|EC876874
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|211469231|gb|FL410779.1|FL410779
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTG
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTG
EST: gi|78091413|gb|DV519787.1|DV519787
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|60349186|gb|DN216159.1|DN216159
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|78026942|gb|DV495329.1|DV495329
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|94476085|gb|EB705043.1|EB705043
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|60344966|gb|DN211939.1|DN211939
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|50325839|gb|CO520965.1|CO520965
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|44682094|gb|CK787142.1|CK787142
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|60344681|gb|DN211654.1|DN211654
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|71434212|gb|DR815262.1|DR815262
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
EST: gi|60338381|gb|DN205354.1|DN205354
EST:     CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG                         GTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA
genomic: CCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGA

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: 179

ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 90

ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 44

ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcct ... actcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttcttctttattaccatttttattagttatccaacttttaactcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC
                                        ttttaac  putative branch site (score: 44)
                                              ctcttgt  CT-rich tract
        ttctttattaccattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacttgttaacaatgtaattttgtttctgttatttgtatgatgttattgttcttctttattaccatttttattagttatccaacttttaactcttgtagGTTCCATCCGTCTTGTATGGGAATGACCATTGAGCAAGCAAAAAAGATAGATCATTACATGTGCTCGGATTGTGCTAAAGAAAATGGTGCAAAGAGACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA