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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctaattgttacattctatctgcatattagatcttggttgatcctagtagctcctatgcatgtaagcatactaagcttttgttttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG

Basic information

species Zea mays
transcript GRMZM2G022061_T05
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022061_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g27840.1 (Oryza sativa), 3'ss of exon 10
gtatgtgctaattgttacattctatctgcatattagatcttggttgatcctagtagctcct------atgcatgtaa----gcatactaagcttttgttt-tttgt-cagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG
||||||  | |||      |||| | ||||     ||  |||    || |||       ||      ||||||| ||    ||||||| || |||||||| | ||| |||||  ||||||||| ||||||||||| || |||||||||||||||||||| |||||||||||||||||||| || || ||||| |||| | |||| ||| |
gtatgtttttattccattcttctgtatgcactaatgaatttgaacaatgctatccatctcttagtccatgcatgcaatgaagcatactcagtttttgtttgtctgtacagTTCGAAAGGACACTGCTGCTGAGATAGCAAAGAAACGAGAACAGGAACGCCAAAGGCAGGAAAAACTTGCGGAGGTAGGTCGGTACAGGGGTCGAAGCAG

upper sequence: GRMZM2G022061_T03 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G05990.1 (Glycine max), 3'ss of exon 9
---------------------------gtatgtgctaattgttacattctatctgcat---attagatctt-----ggttgatcctagtagctcctatgcat---gtaagcatactaagcttttgttt-tttgt-cagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG
                            ||   | | |  |  |  ||||||||||||   | ||  ||||     |  |||  |||| ||  | | || ||   |||    |  |  |    |||||  |||| ||||||| || || || ||||||||  ||||||||||| | |||||||| || || ||||||||||| ||||| |||  | || |||  |  ||   ||| | 
gtatggctgtttgagtaatttattttaataacagatcaacgaaatcttctatctgcattctactaattcttttcaggagtgagtctagcagtacttctgaattttgtatttctgatgtgtaactgtttgcttgtgcagTTAAGAAAGATACTGCTGCTGAACTTGCCAAGAAAAGGGAACAGGAGCGGCAGAGGCAGGAAAAGCTTGCGGAAACTAGTAGATTGAGTCGGTATAGACA

upper sequence: GRMZM2G022061_T03 (Zea mays), 3'ss of exon 10
lower sequence: AT4G36980.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatg-tgctaattgttacattctatctgcatattagatcttggttgatcctagtagctcctatgca-tgtaagcatactaagcttttgttttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG
||| | |  |||||  |   || | | | | |||   ||   | ||  ||||| | |||  |    | ||  |   |       |  |||| |  | ||||||| || ||| | ||  | || |  || ||||||||||||||||| |||||||||| ||| ||||| || |||    | || |  |  ||   ||| | 
gtaagatcttaattact--gttatgtttac-tatc--attaagtttattcctatttgctgttggaaactgagatggtggatgaatcatgttgtacg-cagTTAAGAAAGACTCTGCAACAGAAACGGCTAAGAAACGAGAACAGGAGCGACAAAGGCTGGAGAAACTAGCGGAAACAAGCCGGTTAAGTCGGAATAGGCA

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|6918688|gb|AW400218.1|AW400218
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|93012252|gb|EB637772.1|EB637772
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|89250973|gb|DY622759.1|DY622759
EST:     AAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: AAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|67024598|gb|CO453347.1|CO453347
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|37385048|gb|CF629639.1|CF629639
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|211251413|gb|FL479559.1|FL479559
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGAAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|40335728|gb|CK369798.1|CK369798
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|37388853|gb|CF631641.1|CF631641
EST:     ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
EST: gi|94473364|gb|EB702322.1|EB702322
EST:     ACCCCAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAA                         TTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC
genomic: ACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGAC

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: 155

GTTGCTTCTGGGGGAACTGGTAAAACTCCCCAGACTGAAAAGAAAGAAACACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 164

GTTGCTTCTGGGGGAACTGGTAAAACTCCCCAGACTGAAAAGAAAGAAACACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 170

GTTGCTTCTGGGGGAACTGGTAAAACTCCCCAGACTGAAAAGAAAGAAACACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

GTTGCTTCTGGGGGAACTGGTAAAACTCCCCAGACTGAAAAGAAAGAAACACCACAAGAAAGACTTAAGAGGATAATGAGCAAACAGCTTAACAAGCAAAgtatgtgcta ... tttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcctagtagctcctatgcatgtaagcatactaagcttttgttttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG
 ggttgat  putative branch site (score: 171)
                                      cttttgttttttgtc  putative PPT
                                       ttttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctaattgttacattctatctgcatattagatcttggttgatcctagtagctcctatgcatgtaagcatactaagcttttgttttttgtcagTTAAAAAGGACACGGCTGCTGAGATTGCCAAGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG