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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagtttgtgatggtaggaagaccctgcaacatgatttcgtttatccatatgagatgtttagtactacatgaaagctaatatattgcctgttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC

Basic information

species Zea mays
transcript GRMZM5G830874_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830874_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g08270.3 (Oryza sativa), 3'ss of exon 5
taagtttgtgatggtaggaagaccctgcaacatgatttcgtttatccatatgagatgtttagtactacatgaaag--ctaatatattgcctgttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC
     | ||  |      || |  ||  | | || ||  | || |   | |  | |  |||  |    |||||||  |||||  ||| | ||     | |||||| ||||  ||| |||| ||||||||  | |||||||||||| ||||||| || || |||||||||||| | |||||||| ||||||| ||||||||| 
-ggtgtagtagttcctacaacatgctctatc-tgtttaagattctatctttctgtttcttaccatatgatgaaagttctaatccattccatggctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAATTGACCTGTGTGGTCTTCACGTAAGCGAGGCGATACACGCCCTGAACTAT
















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|211046344|gb|FL092972.1|FL092972
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|20208417|gb|BQ134506.1|BQ134506
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|211046341|gb|FL092969.1|FL092969
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|78124910|gb|DV543294.1|DV543294
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|71418229|gb|DR804377.1|DR804377
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|78110728|gb|DV529126.1|DV529126
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|78543868|gb|DV621366.1|DV621366
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|60400536|gb|DN233343.1|DN233343
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
EST: gi|211376348|gb|FL146641.1|FL146641
EST:     CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAG                         ATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT
genomic: CAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAAT

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: 75

GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 103

GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACAACATATCGACAAAGgtcagatata ... ttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatatgagatgtttagtactacatgaaagctaatatattgcctgttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC
                            agctaat  putative branch site (score: 103)
                                         cctgttccc  putative PPT
                          aaagctaatatatt  TA-rich tract