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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttttccatgctaggatacacctccgcatggggggaagtatctgatctagattacagaattctgtcaaaaacatacctgtacctttgctggactcgatatgtgacgatgttacttccatttgcatggctacgattgatcatccagaacccagcagttactaatcatttgtcgtgtgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTATCAATTGCCAGGTGACTGGGTGCATGTTGGACACAGCACCCAATGGCTG

Basic information

species Zea mays
transcript GRMZM2G563190_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G563190_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g26660.1 (Oryza sativa), 3'ss of exon 8
gttcgttttccatgctaggatacacctccgcatggggggaagtatctgatctagattacagaattctgtcaaaaacatacctgtacctttgctggactcgatatgtgacgatgttacttccatttgcatggctacgattgatcatccagaacccagcagttactaatcatttgtcgt-gtgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTATCAATTGCCAGGTGACTGGGTGCATGTTGGACACAGCACCCAATGGCTG
                                                                                    |    | |    || |  |  |   | || |||      || | |    | |      |||||||||  |||||||  |||||  |    | |  |||| |||||||||||||| || || || || ||||||||||||||||||||||| ||   ||||||||| ||||| ||| | |||||||| ||||||||||||||||| 
------------------------------------------------------------------------------------aagcctaccaatcttgtcacatattgctgatacacgagatttcttttgcatgg-----catccagaatacagcagtccctaatggtcgccctttatgatttacagGTACAGGCACCTTGGCCAGTTTGCTCCACTGGGTGGAGAGCAAACAGCCGCTCAATTGCCGGGTGATTGGATACATGTTGGTCACAGCACCCAATGGCTA
















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|19436415|gb|BM952825.1|BM952825
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|12047088|gb|BF729227.1|BF729227
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|87154011|gb|DY398800.1|DY398800
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|111195878|gb|EE294013.1|EE294013
EST:     AAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: AAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|7135058|gb|AW497895.1|AW497895
EST:     TAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: TAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|87152158|gb|DY396947.1|DY396947
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|78180513|gb|DV550886.1|DV550886
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|148948662|gb|EC898576.2|EC898576
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|8577152|gb|BE129789.1|BE129789
EST:     GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: GGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
EST: gi|7135440|gb|AW498087.1|AW498087
EST:     TAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAG                         GTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA
genomic: TAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTA

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: 24 (upstream exon), 48 (downstream exon)
Score: 2

ACCTAGCCGACTGCTTCAACAGAATGAAGACGTGTGAACAATATCCTGAGGGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTATCAATTGCCAGGTGACTGGGTGCATGTTGGACACAGCACCCAATGGCTG


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 49

ACCTAGCCGACTGCTTCAACAGAATGAAGACGTGTGAACAATATCCTGAGGGTCCTATAAGGATCAGAGGTGCAGGGCGCCATCGGTTCAAACCTTTCAGgttcgttttc ... tgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTATCAATTGCCAGGTGACTGGGTGCATGTTGGACACAGCACCCAATGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgattgatcatccagaacccagcagttactaatcatttgtcgtgtgatgtacagGTACAGGCATCTCGGGCAATTCGCTCCACTGGGTGGAGAGCAAACTGCTTATCAATTGCCAGGTGACTGGGTGCATGTTGGACACAGCACCCAATGGCTG
                           tactaat  putative branch site (score: 49)
                              taatcattt  TA-rich tract