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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatgatccgagtatcattatttattctaaggcattacatcgagtctgaaggatttccaatggcacag

Basic information

species Zea mays
transcript AC205703.4_FGT002
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC205703.4_FGT002 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 5'ss of exon 7
CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatgatccgagtatcattatttattctaaggcattacatcgagtctgaaggatttccaatggcacag
||| ||||| || ||||| |||||||||||||||||||| || |||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||  | | |||  | |  | |  | |  |  ||   || |||  |  |||||      |   || | ||||
CCCTGAGATTTACAACAATGACTTCACCACTCCTTTGCATGTAGTTATTGACAAGTGCATCCAATCATCCCCAATTGACACAAGAAGGGCTCTTTATAAGgtttgtgttatcaaaatgccgtcttatgattcaaaatatcacagtggttctgagtttcattttattggacag
















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|8318635|gb|BE025380.1|BE025380
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGCCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCACAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|32920418|gb|CF025230.1|CF025230
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|74240911|gb|DT648825.1|DT648825
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|30032185|gb|CB834036.1|CB834036
EST:     AAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: AAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|32921953|gb|CF026765.1|CF026765
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|149099376|gb|EE185415.2|EE185415
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|67032896|gb|CO461645.1|CO461645
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|28390221|gb|CB250106.1|CB250106
EST:     CTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: CTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|24769340|gb|CA404469.1|CA404469
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCACAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|71759494|gb|DR957431.1|DR957431
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|32920457|gb|CF025269.1|CF025269
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGACTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|32922282|gb|CF027094.1|CF027094
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|37382936|gb|CF628439.1|CF628439
EST:     CTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATG-TCNAAAGATTTCCACAGGAG
genomic: CTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTC-AAAGATTTCCATAGGAG
EST: gi|32846117|gb|CD985798.1|CD985798
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCAACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|67042751|gb|CO469006.1|CO469006
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|148957989|gb|EC904154.2|EC904154
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
EST: gi|109637254|gb|EC590799.1|EC590799
EST:     ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGAGCTCTTTATAAG                         AATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG
genomic: ACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGG

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), 49 (downstream exon)
Score: 87

CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 78

CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatga ... aatggcacagAATATTGTCCTGTCTGGAGGCTCGACTATGTTCAAAGATTTCCATAGGAGGTTACAGCGGGACCTAAAGAAGATAGTGGATGCACGGGTCCGTGCATCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGGCTCTTTATAAGgttcttatgatccgagtatcattatttattctaaggcattacatcgagtctgaaggatttccaatggcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG