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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagagatgtttcgatgaatactattaccgacgtggccattatgctgtgtgtgggcagcgggactgatgtttggtctgttaactattttgttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG

Basic information

species Zea mays
transcript AC217975.3_FGT001
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217975.3_FGT001 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g44330.1 (Oryza sativa), 3'ss of exon 2
-------ttaa--gagatgtttcgatgaatactattaccgacgtggccattatgctgtgtgtgggcagcgggactgatgtttggtctgttaactattttgttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG
       ||||   ||   |||       |    | |   | |      ||| | |   | | |     |||||||||| | ||| ||||  | || ||     | ||||||||||| |||||||||||||| ||||| |||||||||||||| || ||||||||||   ||||||||||||||||||| |||||||||||||| ||| 
taaatatttaatcaaggaattttcgcagctgaattcattcatgcaaattttaagtttcttattg----tgggactgatggtgggtttgttcgccatatt-----tgaagGTGCGGGATTGGTACTTGGACTCTTTCCGCGACATCAGATACTTTCCAGAAGTGAGGAATAGGAACGACGAGCTCGCTTTTACGCAGATGATCAAGATGA
















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|148949845|gb|EC895336.2|EC895336
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|13558483|gb|BG549839.1|BG549839
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTT
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTT
EST: gi|211237293|gb|FL218655.1|FL218655
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|211239509|gb|FL218657.1|FL218657
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|101384481|gb|EB814285.1|EB814285
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|148943885|gb|EC888965.2|EC888965
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|211239511|gb|FL218659.1|FL218659
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|149077995|gb|EE166733.2|EE166733
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|78178961|gb|DV549334.1|DV549334
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|71442067|gb|DR823117.1|DR823117
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|76915118|gb|DV165833.1|DV165833
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTTCCCTGA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTT-CCCTGA
EST: gi|12046366|gb|BF728505.1|BF728505
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|91051554|gb|EB161972.1|EB161972
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|91051211|gb|EB161629.1|EB161629
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|211237290|gb|FL218652.1|FL218652
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|76292668|gb|DV032236.1|DV032236
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|91055986|gb|EB166404.1|EB166404
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|6918498|gb|AW400028.1|AW400028
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACATGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|13126034|gb|BG316484.1|BG316484
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|149095477|gb|EE181127.2|EE181127
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|148956924|gb|EC902853.2|EC902853
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|78088463|gb|DV516856.1|DV516856
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|149112846|gb|EE295660.2|EE295660
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|149055302|gb|EE156239.2|EE156239
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
EST: gi|91874112|gb|EB404069.1|EB404069
EST:     AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAG                         GTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA
genomic: AGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAA

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), 44 (downstream exon)
Score: 10

GCAGTTCCTGCACAAGGAGCTCCCCATCCGCTTCGCGCGCCGCGCGCTCGAGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 85

GCAGTTCCTGCACAAGGAGCTCCCCATCCGCTTCGCGCGCCGCGCGCTCGAGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

GCAGTTCCTGCACAAGGAGCTCCCCATCCGCTTCGCGCGCCGCGCGCTCGAGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GCAGTTCCTGCACAAGGAGCTCCCCATCCGCTTCGCGCGCCGCGCGCTCGAGCTCGACTCGCTGCCCTTCGGCCTCTCCAACAAGCCCGCCATCCTCAAGgtccgcctcc ... gttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgtgtgggcagcgggactgatgtttggtctgttaactattttgttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG
                                tgttaac  putative branch site (score: 103)
                                         ttttgtt  putative PPT
                                tgttaactattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaagagatgtttcgatgaatactattaccgacgtggccattatgctgtgtgtgggcagcgggactgatgtttggtctgttaactattttgttatttaagGTGCGGGACTGGTACTTGGACTCATTCCGGGACATCAGATACTTCCCTGAAGTGAGGAGCCGGAACGACGAGCTCGCTTTCACGCAGATGATCAATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - -atgtttc
- - - - - - - - - - - - - - - - - - - - -tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtt