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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatctggaaattgagcctaactaccagatcttatgctacattttaaaatataagaatactgaagcttatttttcttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 8
gtgagcatctggaaattgagccta---actaccagatcttatgctacattttaaaatataagaatactgaagcttatttttcttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG
|| || | ||| |  ||||  ||     ||  |||| | | | ||||| || ||  |  ||| ||| |||| |  |   || ||||||||||||||||||||||||||| ||||||||| | ||||||||||| || ||||||||||||||||||| ||||||||||
gtaagtacctgaaggttgaaactgtttgctgtcagaacatttcctacagtt-aagtttcaagcatagtgaatcggaccctttttttcttcagATCAATGTTGTTACACAGCGTGGTTTTATTCCTGTTGATGAGCGAATGCGAGTCATGGATGCAGATGGCAATGTG

upper sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 8
gtgag-catctggaaattgagcctaactaccagatcttatgctacat-------ttta--aaatataagaatactgaagcttatttttcttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG
||  | | ||| | |  | |   ||| ||  | || | |    | ||       || |  ||  | | || |  || |  |    ||  ||| || ||||||| ||| || ||||||||||||||| | ||||||||||| || |||||||| || ||||| | ||| ||| ||
gtatgtcttctagtatatcaatttaattaatatatttgacaaaatatagagatcttcattaacaaaaggatttttggatgtggaattgttttcctacagATCAGTGTAGTAACACAACGTGGTTTTATTCCTGTTGATGAGCGTATGCGAGTAATTGATGCTGATGGAAATCTG
















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|67016819|gb|CO445568.1|CO445568
EST:     TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC                         ATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
genomic: TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
EST: gi|6536537|gb|AW224850.1|AW224850
EST:     TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC                         ATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
genomic: TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
EST: gi|31354606|gb|CD438963.1|CD438963
EST:     TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC                         ATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
genomic: TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
EST: gi|6626525|gb|AW258057.1|AW258057
EST:     TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC                         ATCAATGTTGNTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
genomic: TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
EST: gi|32932110|gb|CF036922.1|CF036922
EST:     TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC                         ATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
genomic: TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAAC                         ATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA
genomic: TTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGA

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: 128

GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 114

GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 217

GTTGACGCAGCCCTTATAGCTACAGGAAGGGCGCCATTCACCAAAGGGCTTGGCTTGGAAAACgtgagcatct ... ttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgctacattttaaaatataagaatactgaagcttatttttcttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG
                                   cttatttttcttttct  CT-rich tract
          attttaaaatataaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatctggaaattgagcctaactaccagatcttatgctacattttaaaatataagaatactgaagcttatttttcttttcttcagATCAATGTTGTTACACAACGTGGTTTTGTGCCTGTTGATGAACGGATGCGAGTCATGGATGCAGGTGGCAATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA