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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgttattagatcacactccaaatctgtgtccccctgtgtatatcagatgtgacatcgtgttatttttatgggtcaatag

Basic information

species Zea mays
transcript GRMZM2G116434_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116434_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os06g49990.2 (Oryza sativa), 5'ss of exon 13
CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgttattagatcacactccaaatctgtgtccccctgtgtata---------------tcagatgtgacatcgtgt----tatttttatgggtcaatag
||| ||||| ||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||| ||||| ||||||| | ||| |  |||| | |   |||     |  ||||||| | |               ||||| |||| | ||| |    |   || |  | | || ||
CCTTGGTGATTGTGGTCGAGCAGCAATCCAGACGCAAGGCTCCATGAATAATCCATTTGGGTCAACTTTTGTCTATGGATATCAGAATATTGCTTTTGAGgtggtttttaattaatcaaa-taagaatagagttttccctgtgcaaactgtattgtcattactcagaagtgaaaccgtttgttctgccttcactgattaacag

upper sequence: GRMZM2G116434_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 5'ss of exon 13
CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggt-gttattagat-cacactccaaatctgtgtc--------cccctgtgtatatcagatgtgac-atcgtgttatttttatgggtcaatag-------------------------------------------------------------------------------------
||| || ||||||||||| || || || || || ||||| || |  ||||||||||||||||| |||||||| ||||||||||| ||| | || || |||||||||  ||  |  || | || ||||  | | |  |        |  || | | |||   | |  || | |    | || | || | |  ||                                                                                       
CCTTGGGGACTGTGGCCGTGCAGCTATTCAAACGCAAGGTTCTACAAACAATCCATTTGGATCTACTTTTGTGTATGGTTATCAAAATGTTGCATTTGAGgtgggttattgatgaatactcaatccatgtgttttgctttggaaacttctttatctattcaaagcaaccaccaccatgttctgattgctttatgtatttcgttaaatggcacaatcaattttcaatttcttcagtttatgggtgaggagattcttaacaaagatcttgctgatactgcag
















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|37377650|gb|CF625447.1|CF625447
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|6695458|gb|AW288566.1|AW288566
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|13126006|gb|BG316681.1|BG316681
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|67024702|gb|CO453451.1|CO453451
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAA-CGGATATATTGCAACTGTCACCCTCTTCNA-TCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|16925040|gb|BM078108.1|BM078108
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|148961880|gb|EE012666.2|EE012666
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|78074282|gb|DV502716.1|DV502716
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|16377490|gb|BI991962.1|BI991962
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|32797638|gb|CD949874.1|CD949874
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|37400992|gb|CF637857.1|CF637857
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|67015496|gb|CO444245.1|CO444245
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCA-TCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|40334237|gb|CK368307.1|CK368307
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|45568491|gb|CK986089.1|CK986089
EST:     AGAAT-TCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: AGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|32787792|gb|CD940028.1|CD940028
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|32798071|gb|CD950307.1|CD950307
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|33467826|gb|CF244875.1|CF244875
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCGATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|5152761|gb|AI759059.1|AI759059
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|67014669|gb|CO443418.1|CO443418
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|60348112|gb|DN215085.1|DN215085
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|12968213|gb|BG265159.1|BG265159
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|71762669|gb|DR960606.1|DR960606
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|78110552|gb|DV528962.1|DV528962
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|76014245|gb|DT941415.1|DT941415
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|84351339|gb|DW245744.1|DW245744
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
EST: gi|101393042|gb|EB818452.1|EB818452
EST:     ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAG                         GTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG
genomic: ATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 49

CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 147

CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

CCTCGGTGACTGTGGCCGAGCTGCAATCCAGACACAAGGCTCCATGAACAATCCATTTGGATCAACTTTTGTATATGGTTATCAGAATATCGCTTTCGAGgtgggtgtta ... gggtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG