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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggagtacttgtgatcatagtggtcttctgttgttttttggtttgaagatattgtgcctgacatcagatttctatttgaattttccttgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC

Basic information

species Zea mays
transcript GRMZM2G047867_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g33710.2 (Oryza sativa), 3'ss of exon 10
--------------------------------------------taatggagtacttgtgatcatagtggtcttctgttgttttttggtttgaagatattgtgc----ctgacatcagatttcta----tttgaattttccttgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC
                                            | ||   ||||||    ||| |   || |    ||      |  |   |   |    | |     ||   |   |||  ||    ||       | |||| || | || | ||| ||||||||||||||||||||||||||||||| |||||||||||| || | |  |||         | ||||||||| 
gttcactaacgttatttaattctgccattctctttcataagctcttattctgtactttccctcaaatatgtatctattttcaccctaatgcaagatttccattcaactttgttgtttaattgttagtcattgatgaactgcttgcttaatagGTTCATCGGGCTGCTTTTGTTCTGCCAACATTTGTAAGGAGAGAACTGGAATCACACAATACT---------TGTGCTGAAAAG
















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|71333305|gb|DR803709.1|DR803709
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|5871424|gb|AW017895.1|AW017895
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|60345911|gb|DN212884.1|DN212884
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|5895598|gb|AW036844.1|AW036844
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTT
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTT
EST: gi|37385273|gb|CF629769.1|CF629769
EST:     AAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: AAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|88757916|gb|DY542057.1|DY542057
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|93014144|gb|EB639664.1|EB639664
EST:     AAGGGAGGCAGCAAAAGCTGGAAGGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: AA-GGA-GCAGCAAAAGCTGGAA-GGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|60350962|gb|DN217935.1|DN217935
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|88757915|gb|DY542056.1|DY542056
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTTTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|71757236|gb|DR955173.1|DR955173
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAA
EST: gi|5847488|gb|AW000567.1|AW000567
EST:     TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAG                         ATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGA
genomic: TAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 64

AGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 85

AGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 148

AGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 163

AGAAGGTCGTGCAGTGAACTTCTTGACTCCTGCGAATCCAATTGAGAAAATAGAAGGAGCAGCAAAAGCTGGAAGGGAACTCAGATTTTACAATTCCGAGgtttgtttag ... tgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagatattgtgcctgacatcagatttctatttgaattttccttgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC
             gcctgac  putative branch site (score: 163)
                                      ttttccttgtttcac  putative PPT
                         atttctatttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatggagtacttgtgatcatagtggtcttctgttgttttttggtttgaagatattgtgcctgacatcagatttctatttgaattttccttgtttcacagATCCATAGGGCTGCTTTTGTTCTGCCAACATTTGTAAGAAGAGAACTGGAAGCATATACCACTCCTATTAGTTCTGCTGAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - -gtacttg
- - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - ttttggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctga