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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactatttgacttgctcttctctgataatactctttcctaatgccagaatcgcactgcctcatgttgttctctgattaattaacaagtacatttgatgttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 3'ss of exon 4
gtaatactatttgacttgctcttctctgataatactctttcctaatgccagaatcgcactgcctcatgttgttctctgattaattaacaagtacatttgatgttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT
                |  | | |||    | |  ||  |||           ||    || | |||   ||||      |  ||| ||| |   ||   | ||  |||||||||||||  | ||||||||||||||||||||||| ||||||||||||||||||
---------------gtaatgtcctccttaagtcttccatccagtattttttgtcattttgacacataa-gttca-----tgcttaccaaatgtgttcctttttcatgcagGAGGATTTCGAAAAGTTGGTCTCCAACTTCCGTCGCATAAGATTTGAATCTACT

upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 4
gtaatactatttgacttgctcttctctgataatactctttcctaatgccagaatcgcactgcctcatgttgttctctgattaattaacaagtacatttgatgttgt-tgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT
                             ||||   ||     | |         |   ||  |  |||  || |   ||   ||| ||| |   |||  | ||   |||||||||||||  | |||||||| |||||||||||||| || |||||||||||||||
----------------------------gtaatgtcctccttaagtcttccgtctggtatgtttt-tgtcattttgacat-gcttaccaaatgtgttttttttttcatgcagGAGGATTTCGAAAAGTTGGTTTCCAACTTCCGTCGCATGAGATTTGAATCTACT
















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|91876333|gb|EB406290.1|EB406290
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|148966783|gb|EE017871.2|EE017871
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|32916159|gb|CF020971.1|CF020971
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|148952245|gb|EC898050.2|EC898050
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|78080728|gb|DV509140.1|DV509140
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|148966141|gb|EE017084.2|EE017084
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|71448119|gb|DR829169.1|DR829169
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|148938292|gb|EC882596.2|EC882596
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAAAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|32940949|gb|CF045768.1|CF045768
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAATCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|71770930|gb|DR968867.1|DR968867
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTCCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|14191192|gb|BG833422.1|BG833422
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|93016572|gb|EB642092.1|EB642092
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
EST: gi|94477192|gb|EB706150.1|EB706150
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAAGT-GGTCTCCAACTTCCGTCGGATAAGATTTGAATC
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAA-GTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATC
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTAT                         GAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT
genomic: ATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCT

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: 105

CTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT


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

CTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

CTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

CTGTTCTGCAACTTATGACACTGTTAGCCTGCTGAAAGATGCTGTGGATCATGGATGCTGTGTCGTATTGGCAAACAAGAAACCTCTTACCGGTGCTTATgtaatactat ... gttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgcctcatgttgttctctgattaattaacaagtacatttgatgttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT
                      attaattaacaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatactatttgacttgctcttctctgataatactctttcctaatgccagaatcgcactgcctcatgttgttctctgattaattaacaagtacatttgatgttgttgcagGAGGATTTTCAGAAGTTGGTCTCCAACTTCCGTCGGATAAGATTTGAATCTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT