Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtcgttccatcaaaagctattgacaatgcaggatctttgtttaatatgccataatgttattttatttgagattcttatactgaaaaattcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA

Basic information

species Zea mays
transcript GRMZM2G088974_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088974_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g08270.1 (Oryza sativa), 3'ss of exon 4
ggtgtcgttccatcaaaagctattgacaatgcaggatctttgtttaatat-gccataat-------gttattttatttgagattcttatactgaaaaattcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA
    |  ||  || |||||   |   |  ||||  | ||||  ||| ||| | ||| ||       |  ||||  |||   || |  | | |       |  ||||||||||||||||||||| || |||||| ||| ||||| | |||| || || |||||||| ||| |||| |   ||| ||| ||||||||||| || ||||||
----ttattg-ataaaaagtagtgtcctgtgcaaaaccttttgttactattggcatgattcactaaggaatttcctttataatcccaacatttgtg---ttaatgcagTTTCATAAGGGGAGACCAATATGCAATTGGACTTGCATTACTGGACGAAGGCAAAGTAGTTTTGGGAGCAATGGCATGCCCAAATCTTCCTTTCAAATCA
















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|149080861|gb|EE169941.2|EE169941
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|76013309|gb|DT940479.1|DT940479
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|6564144|gb|AW231766.1|AW231766
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|60672399|gb|DN475149.1|DN475149
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|24961621|gb|CA483621.1|CA483621
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|86467595|gb|DY233965.1|DY233965
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|6587603|gb|AW244921.1|AW244921
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|71766943|gb|DR964880.1|DR964880
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|93282631|gb|EB674895.1|EB674895
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|67018692|gb|CO447441.1|CO447441
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|71762698|gb|DR960635.1|DR960635
EST:     TAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: TAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|50334941|gb|CO530067.1|CO530067
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|40333919|gb|CK367989.1|CK367989
EST:     GGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|71439240|gb|DR820290.1|DR820290
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|76937581|gb|DV175190.1|DV175190
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|101401653|gb|EB822491.1|EB822491
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
EST: gi|32929559|gb|CF034371.1|CF034371
EST:     GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGG                         TTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG
genomic: GGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGG

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: 160

TATCTAAGGAAGATGTGCTTTCTGCAATTGATGGTGGTAAATCTGAGGGAGGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 90

TATCTAAGGAAGATGTGCTTTCTGCAATTGATGGTGGTAAATCTGAGGGAGGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TATCTAAGGAAGATGTGCTTTCTGCAATTGATGGTGGTAAATCTGAGGGAGGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

TATCTAAGGAAGATGTGCTTTCTGCAATTGATGGTGGTAAATCTGAGGGAGGTCCATCTGGGCGACATTGGATATTAGACCCAATAGATGGCACTAAAGGgtgagtttga ... ttcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatgccataatgttattttatttgagattcttatactgaaaaattcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA
 gtttaat  putative branch site (score: 115)
        ataatgttattttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgtcgttccatcaaaagctattgacaatgcaggatctttgtttaatatgccataatgttattttatttgagattcttatactgaaaaattcgatgcagTTTCATAAGGGGAGATCAGTATGCAGTTGCACTTGGACTACTTGATGAGGGCAAAGTTGTTCTGGGTGTGTTGGGATGTCCAAATCTTCCATTAAAATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - catcaaa
- - - - - - - - - gctattg
- - - - - - - - - - - - - - atgcagg
- - - - - - - - - - - - - - - - - - - - - - - -tatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaaaaa