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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaattccttgtgccatccatttttattccttgaatgtgattcggagccgcacattatttcattaaagatgtttgcactccccattatggtaggtgtaaccgttattcatgcagccattttctttgtgtttttcttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG

Basic information

species Zea mays
transcript GRMZM2G031802_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 4
gtatgaattccttgtgccatccatttttattccttgaatgtgattcggagccgcacattatttcattaaagatgtttgcactccccattatggtaggtgtaaccgttattcatgcagccattttctttgtgtttttcttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG
                                                    | |    | | ||| |       || |  | ||  || |  | | | |    | |  || |  | |  || | |   |  |||| ||    |||| ||| | || || || ||||| ||||| |||||||||||||||||||  ||||||||||||||
----------------------------------------------------gtatgg-actccatcat-----cttacctttccatttctcatggttatggtggatgatcttttaactgttatat--atacttttgttg---cagGCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG
















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|7136004|gb|AW498376.1|AW498376
EST:     CCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: CCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|148995872|gb|EE035110.2|EE035110
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|71425662|gb|DR806812.1|DR806812
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|211132529|gb|FL458973.1|FL458973
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|60397063|gb|DN229882.1|DN229882
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|5361053|gb|AI795668.1|AI795668
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|60359236|gb|DN226209.1|DN226209
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|71425663|gb|DR806813.1|DR806813
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|71329461|gb|DR801451.1|DR801451
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGGCAA-CTCTGTTGTATGCTGACTTCTTCTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTG-CAAACTCTGTTGTATGCTGACTTCTTCTTT
EST: gi|78117678|gb|DV536065.1|DV536065
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|8383313|gb|BE056256.1|BE056256
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|5847439|gb|AW000518.1|AW000518
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|67022873|gb|CO451622.1|CO451622
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
EST: gi|78117677|gb|DV536064.1|DV536064
EST:     TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAA                         GTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT
genomic: TAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTT

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: 47 (upstream exon), 47 (downstream exon)
Score: 84

TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 109

TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 142

TGCCTACCGTGTGCTTTATATCCTTAACTGGATTTACCGATACTTCACTGAGCCCCATTTTGTCCACTGGATAAgtatgaattc ... cttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaggtgtaaccgttattcatgcagccattttctttgtgtttttcttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG
                                            tcttaac  putative branch site (score: 142)
                          ccattttctttgtgtt  CT-rich tract
                                        tttttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaattccttgtgccatccatttttattccttgaatgtgattcggagccgcacattatttcattaaagatgtttgcactccccattatggtaggtgtaaccgttattcatgcagccattttctttgtgtttttcttaacccagGTTGGATGGCAGGAATAGTGCAAACTCTGTTGTATGCTGACTTCTTCTTTTATTACATAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG