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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcctgctgcttatttattcatgataacttacagactagcttgagcataattctatatctatgaatattattatttcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG

Basic information

species Zea mays
transcript GRMZM2G047404_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047404_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g12600.1 (Oryza sativa), 3'ss of exon 6
gtgagtatcctgctgcttatttattcatgataacttacagactagcttgagcataattctatatctatgaatattattatttcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG
||||| | | || |  ||| ||||    || || || |    ||  |   |  |  | | || | |  || |||| || |||||| || ||||| ||||||| |||||| |||||||||||||| |||||||||| ||||| ||||||||||||||||||
gtgagcaccttgatatttaattata---gacaaattgctccttacatattgtttggtgcaattttt--gactatt-ttctttcttatgtagGGTCTGAACTTAAAACAGATATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAG

upper sequence: GRMZM2G047404_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 3'ss of exon 6
gtgagtatcctgctgcttatttattcatgataacttacagactagcttgagcataattctatatctatgaatattattatttcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG-------------------------------
||||| | | || |  ||| ||||    || || || |    ||  |   |  |  | | || | |  || |||| || |||||| || ||||| ||||||| |||||| |||||||||||||| |||||||||| ||||| ||||||||||||||||||                               
gtgagcaccttgatatttaattata---gacaaattgctccttacatattgtttggtgcaattttt--gactatt-ttctttcttatgtagGGTCTGAACTTAAAACAGATATACACAAGGTCACTGATTGCTGCGTTCTGTTTCCATGCATACCAACAGGTCAGCCATCTAATTGATTTTCTAAAAATAG
















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|37395421|gb|CF634991.1|CF634991
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|8103136|gb|AW927794.1|AW927794
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|40336776|gb|CK370846.1|CK370846
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|60395055|gb|DN227924.1|DN227924
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|116814527|gb|EC857099.1|EC857099
EST:     CCTTACTTACAGAAGGTGTTCAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|67026165|gb|CO454914.1|CO454914
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|23199512|gb|BU582077.1|BU582077
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|211071461|gb|FL174369.1|FL174369
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|23199513|gb|BU582078.1|BU582078
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|14191027|gb|BG833257.1|BG833257
EST:     TTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAGCTTGAAACAGGTATACTCAAGGTCATTGATTGCTGCATTCTGC
genomic: TTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|33103829|gb|CF063789.1|CF063789
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|7844570|gb|AW787792.1|AW787792
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|37384374|gb|CF629256.1|CF629256
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|211145645|gb|FL480700.1|FL480700
EST:     TAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: TAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|9028527|gb|BE238522.1|BE238522
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|12046824|gb|BF728963.1|BF728963
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|76281902|gb|DV021470.1|DV021470
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
EST: gi|110527946|gb|EE032130.1|EE032130
EST:     CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCT                         GGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC
genomic: CCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGC

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), 48 (downstream exon)
Score: 296

CCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

CCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

CCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 546

CCTATTCTCGATCATTACAGTCATGTCATTCTTCCTGTTGGCCCCAGTAACCTTACTTACAGAAGGTGTTAAAGTTAGTCCAGCAGTGTTGCAGTCTGCTgtgagtatcc ... tcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagactagcttgagcataattctatatctatgaatattattatttcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG
 aacttac  putative branch site (score: 546)
                                        ttatttctt  putative PPT
                ataattctatatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatcctgctgcttatttattcatgataacttacagactagcttgagcataattctatatctatgaatattattatttcttgtgcagGGTTTGAACTTGAAACAGGTATACACAAGGTCATTGATTGCTGCATTCTGCTTCCATGCATACCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC