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

gtatgttccgctcagcacattttgcgagaaaaataaagcctacaataagtaagttttctaattaatggcgtgatttcttaccgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAACTCATGCCGGCCCCATCGACAATCTCTTGACACACCTTTCGGACCCGTT

Basic information

species Zea mays
transcript GRMZM2G103101_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103101_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g52650.1 (Oryza sativa), 3'ss of exon 5
-----gtatgttccgctcagcacattttgcgagaaaaataaagcctacaataagtaagttttctaattaatggcgtgatttcttaccgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAACTCATGCCGGCCCCATCGACAATCTCTTGACACACCTTTCGGACCCGTT
          || | || || ||| |||||  | || ||||| || | | ||| ||    |  |  ||  |  | |||| |   || ||||||||||||||||| ||||| || |||||||| || || ||||||||||| || |||||||  || || ||||||||||| |||||||| ||||| ||||||||
gtagctccactttctctaagtacagtttgcttgcaacataaatcc-atagtaa-tagtcatagt--ttgctaacatgatctacgactgtcacagGGAGGTTGGCTATGGTTGCTATGCTTGGGTTTATTGTGCAAGCATCTGTGACTCATGTTGGACCAATCGACAATCTTTTGACACATCTTTCAGACCCGTT
















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|148995803|gb|EE035034.2|EE035034
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|149100655|gb|EE186743.2|EE186743
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|4730640|gb|AI649806.1|AI649806
EST:     GAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: GAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|94472956|gb|EB701914.1|EB701914
EST:     ACAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGGTGGCTATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|32850382|gb|CD990063.1|CD990063
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCTGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|13126211|gb|BG316781.1|BG316781
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|13558835|gb|BG550190.1|BG550190
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|149100656|gb|EE186744.2|EE186744
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|16927444|gb|BM080513.1|BM080513
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|148994267|gb|EE034026.2|EE034026
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|148995804|gb|EE035035.2|EE035035
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|161407243|gb|DW042299.1|DW042299
EST:     CATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: CATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|148967697|gb|EE018962.2|EE018962
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCANAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|148987230|gb|EE031063.2|EE031063
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
EST: gi|16919006|gb|BM073997.1|BM073997
EST:     AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACG                         GGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA
genomic: AAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAA

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 2 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 93

CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAACTCATGCCGGCCCCATCGACAATCTCTTGACACACCTTTCGGACCCGTT


Block sizes: 44 (upstream exon), 35 (downstream exon)
Score: 16

CTACCCCGGGGGTCCACTGTTCAATCCACTAGGACTCGCAAAGGATATAGAGAATGCTCATGACGAGAAGCTCAAAGAAATCAAGAACGgtatgttccg ... accgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAACTCATGCCGGCCCCATCGACAATCTCTTGACACACCTTTCGGACCCGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagcctacaataagtaagttttctaattaatggcgtgatttcttaccgtcacagGGAGGTTGGCAATGGTAGCCATGCTTGGCTTCATGGTGCAAGCATCCGTAACTCATGCCGGCCCCATCGACAATCTCTTGACACACCTTTCGGACCCGTT
                                        ttcttac  putative branch site (score: 16)
                                       tttcttacc  CT-rich tract
         aataagtaagttttct  TA-rich tract