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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacatcttagtcatggcatggcgctacaatctgttttccactgtgtttaatgtgaacaaaacatcaatggtatttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG

Basic information

species Zea mays
transcript GRMZM2G107654_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 7
gtatgtacatcttagtcatggcatggcgctacaatctgttttccactgtgtttaatg---tgaacaaaacatcaatggta----tttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG
|||||||   | | ||  || ||||    || | | |  ||  ||||   |||       |    |  || | ||| ||     || ||||| |||||||  |||||||||||||||| |||||||| |||||||||||||| ||||| ||||| |  || |||||||| |||||||||||||| ||||||||||
gtatgtattccctcgt-gtgtcatgtaattagatttt--ttatcactacttttgggttattaggtatgacttaaattgtgatgcttcttttatagGGAGTTTTGAGGGTGAACCAGAACATTGAAGTCCGCCCTGGCATTGTAATGAAGGATGAAAGCGGCAACATCAAATGCACCCCAATCTATTCAAGGATTG

upper sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 7
----gtatgtacatcttagtcatggcatggcgctacaatctgttttccactgtgtttaatgtgaacaaaacatcaatggtatttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG
    || |   |  ||    |||          |  |||| ||  |    | |||| | | ||| |  ||    ||||    ||  || ||||||||  ||||||| |||||||| |||||||||||||| || ||||| ||||| |||||||  || |||||||| |||||||||||||| || ||||| |
gtatgtgttctctcctgtaacataattaaatattttaatcagtagttttttatgttaagtatgagctgaatggtaatg---cttcgttccagGGAGTTTTGAGGGTTAACCAGAACATTGAAGTTCGCCCGGGAATTGTAATGAAGGATGAGAGCGGCAACATCAAATGCACCCCAATCTATTCGAGGATCG
















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|211112537|gb|FL352687.1|FL352687
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|33094733|gb|CF054727.1|CF054727
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|28930895|gb|CB334256.1|CB334256
EST:     CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|32934438|gb|CF039250.1|CF039250
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|28873829|gb|CB329766.1|CB329766
EST:     CAGAGGTCGATGAAATCAGGGGTGG-GTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|211525170|gb|FL316542.1|FL316542
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|211070003|gb|FL340001.1|FL340001
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGCAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|32930840|gb|CF035652.1|CF035652
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|16927572|gb|BM080641.1|BM080641
EST:     CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|31357361|gb|CD441718.1|CD441718
EST:     CAGAGGTCGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|32933324|gb|CF038136.1|CF038136
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|33094840|gb|CF054834.1|CF054834
EST:     CAGAGGTTGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATG
EST: gi|166650380|gb|EG220275.1|EG220275
EST:     CAGAGGTCGATGAAATTAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGG                         GGAGTCCTGAGGGTGAACCAGAAGA
genomic: CAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGA

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: 377

ACCTCCCAACATGATTGTTATTCGCTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

ACCTCCCAACATGATTGTTATTCGCTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

ACCTCCCAACATGATTGTTATTCGCTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG


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

ACCTCCCAACATGATTGTTATTCGCTCCTTTGATGTTAACAAGCCTGGTTCAGAGGTCGATGAAATCAGGGGTGGTGTAGCTGGTGGTAGTATTCTCAGGgtatgtacat ... ttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgttttccactgtgtttaatgtgaacaaaacatcaatggtatttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG
                gtttaat  putative branch site (score: 269)
                                          tattttttt  putative PPT
                                     aatggtattttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacatcttagtcatggcatggcgctacaatctgttttccactgtgtttaatgtgaacaaaacatcaatggtatttttttacagGGAGTCCTGAGGGTGAACCAGAAGATTGAAGTTCGCCCTGGCATTGTCATGAAAGATGAGACTGGAAACATCAAGTGCACCCCAATCTACTCAAGGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG