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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgctttggtggtctctctgggatggtttttcctcaacctgtggctgatggtctaaacatggactgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC

Basic information

species Zea mays
transcript GRMZM2G063949_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 8
---------gtatttgct--ttggtggtctctctgggatggtttttcctcaacctgtggctgatggt--ctaaacatggactgaaatgt---agGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC
         || ||   |     ||  | ||| ||   |  |  ||    |||| |||| | ||  |  | ||| || || | || |||   ||||||||| || ||||| |||||||||||| |||||||||||||| |||| || ||||||||||| |||||||||||| | |||||||||||||| |||||
gtatttactgtcttcaataacctgttatgtctatgttgtactagttgggtaaccagtggttcataataaccaaatattgattcaactgttctagGTTGGAATCCGAAGACCCCTCTCAAGGATTTGCTGGAGACAACATTGACCTACCAGCACAAGACTTACAAAGAAGCTATCAAAAGGCAAATGTCACAGGC
















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|93281900|gb|EB674164.1|EB674164
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|40337281|gb|CK371351.1|CK371351
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACGCTGACGT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|32868566|gb|CF008248.1|CF008248
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACGCTGACGT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|149086196|gb|EE175736.2|EE175736
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATTTGCTGGAGACAACACTGACAT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|7137694|gb|AW499223.1|AW499223
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACGT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|211216490|gb|FL245940.1|FL245940
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACGCTGACGT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|60353566|gb|DN220539.1|DN220539
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|21809589|gb|BQ667907.1|BQ667907
EST:     AAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACGT
genomic: AAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|149098033|gb|EE183980.2|EE183980
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACAT
EST: gi|211213926|gb|FL245933.1|FL245933
EST:     TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAG                         GTTGGAACCCAAAGACGCCTCTCAAGGATCTGC
genomic: TGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGC

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: 199

GAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

GAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

GAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

GAGCCCATGATTGACGTGAGCTCGAGTCAGTTCTACGGTGAAGGATACGATGATAGCGACAAGAGGATCCCCGACATGACTATAATCAACAAGCAGCTAGgtatttgctt ... tgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggatggtttttcctcaacctgtggctgatggtctaaacatggactgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC
                               gtctaaa  putative branch site (score: 111)
                                  taaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgctttggtggtctctctgggatggtttttcctcaacctgtggctgatggtctaaacatggactgaaatgtagGTTGGAACCCAAAGACGCCTCTCAAGGATCTGCTGGAGACAACACTGACATATCAGCACAAGACATACAAAGAAGCTGTGAAAAGGCAAATGTCGCAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG