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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

Basic information

species Zea mays
transcript GRMZM2G087692_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087692_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 3'ss of exon 2
---catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
     | |   | | | | ||||   ||   ||||   |   |  |    |  |     || ||||  ||| |  | |||||||||||| ||||  |||||||||| ||||||  |||||| || |||||||| |||||||||||||||||||||||||||||||||||||||
gcagttctcacaattatttagtttaagtcaaacaa-tgtttcccgatcttcctatctgcatattgct-catgtcattattaatgtggtt-atggtctctgaagCTCGCAGGATACGATAATAAGTTGTCTTGGGCTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

upper sequence: GRMZM2G087692_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G43650.1 (Glycine max), 3'ss of exon 3
catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
               || || |  |      |   || |    | ||| |       | ||| |   ||  || | | || |  ||  |  ||| || |||||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||
--------------gcaattataat----tgattttatttcatgtcacgcttttctgttttggattgtt--cttacttatata-ttggtttgtt-tgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG

upper sequence: GRMZM2G087692_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G37130.2 (Glycine max), 3'ss of exon 4
-catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
 ||  ||| | ||| |   || || ||||||     |  |  |         ||  | |||| |     |||   |||  | ||          | || |||||   ||||||| |  | || ||  | ||||| || ||||| |||||||| ||||||||||||||||||
gcaattataattgattttatt-tcatgtcacgcttttcctgttt------tggattgttcttac-----ttagatattggtttg----------tttgcagCTCTGTGGATTTGGTTGTTAGTTGCTTGGGACTACACTGGACTAATGATCTGCCTGGAGCAATGATACAG

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|50328095|gb|CO523221.1|CO523221
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         ------G-ATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|87157627|gb|DY402416.1|DY402416
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|101393422|gb|EB818643.1|EB818643
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|89762249|gb|DY689931.1|DY689931
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|71440891|gb|DR821941.1|DR821941
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCCTGTCTTGGACTTCATTGGACAAATGATC
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGC-TGTCTTGGACTTCATTGGACAAATGATC
EST: gi|22819976|gb|BU500066.1|BU500066
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|13316098|gb|BG410545.1|BG410545
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|78078319|gb|DV506734.1|DV506734
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|74241982|gb|DT649896.1|DT649896
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|26560078|gb|CA832313.1|CA832313
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|26456098|gb|CA827681.1|CA827681
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         CTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
EST: gi|93282992|gb|EB675256.1|EB675256
EST:     GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAG                         ------G-ATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT
genomic: GAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCT

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: 41 (upstream exon), 48 (downstream exon)
Score: 35

ATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 12

ATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 26

ATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 43

ATATGGTGAAGAAGTGGCGAGAGTCAGAGAATGCCACTGGTGATGGGCCTGAGACCCACTTTGTTATCGGCGATGAGGAGTTTCTTCCAATCAAAGAGAGgtgatttcac ... ggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG
                            cattaat  putative branch site (score: 43)
                     atttactcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtatgagtgagtcagttgtcgtgtcacaagcataatcatagacacacagacagatcttgcaacatttactcattaatgtggttcatgggttctgaagCTCACAGGATTTGATAATGAGCTGTCTTGGACTTCATTGGACAAATGATCTACCTGGAGCAATGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA