Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgatcaattgtggttgctatatattgaatatggcttatgcttattttttgggtacattttgaatagcttttatattttcaatcatttctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA

Basic information

species Zea mays
transcript GRMZM5G811223_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 20
tttctgatcaattgtggttgctatatattgaatatggcttatgcttattttttgggtacattttgaatagcttttatattttcaatcatt---tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
    || | ||   ||||     ||   |   |||    ||||||  |||||   |    | ||   ||   || ||   ||   |  ||   ||  |||||| ||||||||||| || || |||||||||||||| |||||||| ||||||||||| || |||||||| || ||||||||||||||||||||| ||||||| 
gacttgcttaa--atggtacacctaagctatttatactatatgct-gtttttaatgccattattatctaatcttaattcctttgctttttttgtcattaccagTGGGCAAAGCAATGCAAAAATTGAAGAGCTTCTGCAAGAGGACCATAATGCTAAACGTAGAAGGGAAAAATACCAAAAACAATCATCTCTCTTGTCAAAG

upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 20
--tttctgat-caattgtggttgctatatattgaatatggcttatgcttattttttgggtacattttgaatagcttttatattttcaatcatttctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
  | | || | || || ||  || ||   |     | |  | | |  ||  |||   | |    | ||  || | |||   ||||  ||  || |   |  || |  |||||||  ||||||||||| || || |||| ||| ||||| |||| |||||||||||||||      ||| ||||||||||| || || || |||
tctgtatgttacagttttgtatgataataacaattttttacatttagttgctttgatgttggtctctgtttaacattt---ttttgtatgtttccgtgattagTGCTCAAAGCACGGCTAAGATTGAGGAACTGCTTCTAGAAGATCAAAATGTTAAGCGCAGAAGGGATCGAATCCAGAAACAATCATCCCTTCTCTCGAAA
















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|211235187|gb|FL451894.1|FL451894
EST:     AGAAAGCAAAGGAAGACATGCTTACCCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: AGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|37374813|gb|CF623795.1|CF623795
EST:     GAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211235185|gb|FL451892.1|FL451892
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211346182|gb|FK944396.1|FK944396
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATASAGCTCGATVNG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211348570|gb|FK944397.1|FK944397
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211249289|gb|FL482046.1|FL482046
EST:     CCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: CCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|32937777|gb|CF042596.1|CF042596
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAATGCTAAGATTGAAGAGCTGCTTCAAGAGGACCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211235186|gb|FL451893.1|FL451893
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|31348909|gb|CD433266.1|CD433266
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211346179|gb|FK944393.1|FK944393
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211346181|gb|FK944395.1|FK944395
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211348571|gb|FK944398.1|FK944398
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211346180|gb|FK944394.1|FK944394
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATANG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211348572|gb|FK944399.1|FK944399
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|211132354|gb|FK982421.1|FK982421
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
EST: gi|67010855|gb|CO439604.1|CO439604
EST:     GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG                         CGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC
genomic: GTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGC

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: 507

GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 445

GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 567

GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 301

GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAGgttgattttc ... tctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttttgggtacattttgaatagcttttatattttcaatcatttctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA
                                        tcatttctct  CT-rich tract
              attttgaatagctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgatcaattgtggttgctatatattgaatatggcttatgcttattttttgggtacattttgaatagcttttatattttcaatcatttctctaccagCGGGCAAAGCAACGCTAAGATTGAAGAGCTTCTTCAAGAGGATCATAATGCTAAGCGCAGAAGGGAGAAGTACCAAAAACAATCATCTCTCCTGTCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
tttctga
- - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tacattt