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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgctttttcgtgaacccccctcccttcttctattgccctcgctgcattaacattgtatgcttttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG

Basic information

species Zea mays
transcript GRMZM2G061419_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 6
---------------gtctgctttttcgtgaacccccctcc---------cttcttctattgccctcgctgca-ttaacattgtatgcttttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
                |||   ||| | ||   ||| |             || |  |||  | ||| ||  | |||||   ||||    |||   ||  |||||||| || |||||||| || ||||||||||||||||||||||| ||||| |||||||||||||| || || ||||||
gtttgcttatcctgaatctctctttccctggttccctccttaactgaatgtttttcttatgcctctctctcaacttaactgggtatttgcttgcatctaccagATATTCATCCAAACTGGCTACCCCCTTGACTTACCTTCTGGCAGCTTGGGAAGCTATTGCATATACGAGTATCACATG

upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------gtctgctttttcgtgaacccccctcccttcttctattgccctcgctgcattaacattgtatgcttttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
                                                    |     | ||  |    || | | |||    | |||    | | | || |    |    || | |  ||| |  ||||||||||| ||||| ||||| || ||||| || |||||||| ||| | || || || ||||| ||||||||||| |||
gtatagcttaaaagaatttgttttcttgtggttgttttctttaggtgtttaattgaaatatttatagttccacttgcctaaaaccatt----tggttacactctt-tcaactgttatcatgcttaacagATATTTATTCAAACCGGATACCCTCTTGATTTGCCTTCTGGAAGTCTAGGGAGTTACTGCATCTATGAATACCATATG

upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------gtctgctttttcgtgaacccccctcccttcttctattgccctcgctgcattaacattgtatgctt--ttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
                                                                     | |      | |    ||     |  ||| |    ||  ||| |||    |   |    |  |  |  || |||||||||||| |||||||| ||||| || ||||| || ||||| | | | || || |||||||| ||||| |||||||||
gtggtacccaaactacagaaatcctgaactaattggcttaattctgtgtctgtttacatttatcaaagacatagctaaggataggcccttaattatctttccttctgtctgaatttgtttaacagatatagtgatttcttgcagATATTTATTCAAACTGGGTATCCTCTAGACTTGCCGTCTGGGACTCTTGGGAGTTATTGCATCTATGAGTACCACATG

upper sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g03130.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------------------------------------------------------gtctgctttttcgtgaacccccctcccttcttctattgccctcg--ctgcattaacattgtatgcttttgt----gcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
                                                                                                  | ||  |  |  |||       |  | |    |      || |     | ||   || || || |||||     | |  |||||||||||| ||||| |||||||| ||||| || |||||||| ||||| || || || ||||| || ||||| || |||
gtgtatttatgcacataaactaccatgccttttatctatgtaacttgcatttttatctaatcttgtttgatattttttccccttttgtgttttttttatatgtgtacttatgattttggttggcattgattggaattctggaatgcccttttaatggtctgattttgctggagacgtgcagATATTTATTCAAACCGGATATCCTCTTGATTTGCCTTCTGGAAGTTTAGGAAGTTACTGCATTTACGAATATCATATG

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|71427423|gb|DR808473.1|DR808473
EST:     ATCCTGCGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGCATATCCCCTTGACTTACCTTCTG
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTG
EST: gi|149075471|gb|EE163995.2|EE163995
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|76913089|gb|DV165003.1|DV165003
EST:     ATCCTGGGACTATCGGAGCTCTCACAAA-GAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACTTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|74245609|gb|DT653523.1|DT653523
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|61119317|gb|DN560278.1|DN560278
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|78090711|gb|DV519085.1|DV519085
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|148972415|gb|EE023349.2|EE023349
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|71304141|gb|DR788190.1|DR788190
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGC
EST: gi|148965663|gb|EE016513.2|EE016513
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGATTCCTGAG                         ATATTTATACCAACTGGATATCCCCTTGACTTACCCTTCTGGCAGTTTGGG
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACC-TTCTGGCAGTTTGGG
EST: gi|76293199|gb|DV032767.1|DV032767
EST:     ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAG                         ATATTTATACAAACTGGATATCCCCCTGACCTACCTTCTGG
genomic: ATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGG

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: 334

GCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

GCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 269

GCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAATGGAGAAGAATCCTGAGgtctgctttt ... tgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccttcttctattgccctcgctgcattaacattgtatgcttttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG
                        cattaac  putative branch site (score: 269)
                                       cttttgt  putative PPT
                         attaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgctttttcgtgaacccccctcccttcttctattgccctcgctgcattaacattgtatgcttttgtgcctggcagATATTTATACAAACTGGATATCCCCTTGACTTACCTTCTGGCAGTTTGGGCAGCTATTGCATATATGAATACCACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT