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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaatttattgtgtgaaaaggaagtttttgtcttgaatgtgatatttatggatgataattgaccaaggaagttttgcattatcattctacactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG

Basic information

species Zea mays
transcript GRMZM2G057056_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057056_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g34770.1 (Oryza sativa), 3'ss of exon 6
------tcaaatttattgtgtgaaa---aggaagtttttgtcttgaatgtgatatttatggatgataattgaccaaggaagttttgcattatcattctacactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
      | | ||||| | | ||  |   |  ||||   ||  |||  | ||    | |||||  ||  ||    ||||  |  ||   |  ||||| |       |||||| || ||||| ||||||||||||||||||||  | | | ||
agtagataatatttaatttctgccagtcaaaaagtaactggattgtgtatgtatatcatggaaaat--ttagttaaggttgccttttgtcgtcatttt-------gcagGTGTACTTCCATGATATACCAGATGAGGTCATTGAAAACCTG
















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|28911394|gb|BM351713.2|BM351713
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|28911370|gb|BM340835.2|BM340835
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|28985527|gb|CB350686.1|CB350686
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|28911294|gb|BM351042.2|BM351042
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|37401613|gb|CF638174.1|CF638174
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|211433116|gb|FL461630.1|FL461630
EST:     TAACTAATCTTACAACTGGRAARAGACTTGRAAGTTTGGACAAAGCTGAG                         GTTTATTTCCMCGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|28911464|gb|BM349702.2|BM349702
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|28911286|gb|BM339599.2|BM339599
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|28911265|gb|BM350764.2|BM350764
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
EST: gi|88752936|gb|DY537077.1|DY537077
EST:     TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAG                         GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
genomic: TAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG

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: 44 (upstream exon), 42 (downstream exon)
Score: 14

GCTATTCCGGAGGTCACGTGTCAACTGTTGGGTCTGTTGTTGTAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 17

GCTATTCCGGAGGTCACGTGTCAACTGTTGGGTCTGTTGTTGTAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 15

GCTATTCCGGAGGTCACGTGTCAACTGTTGGGTCTGTTGTTGTAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 9

GCTATTCCGGAGGTCACGTGTCAACTGTTGGGTCTGTTGTTGTAACTAATCTTACAACTGGGAAGAGACTTGGAAGTTTGGACAAAGCTGAGgcaattttca ... cactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatggatgataattgaccaaggaagttttgcattatcattctacactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG
            aattgac  putative branch site (score: 9)
       atgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaatttattgtgtgaaaaggaagtttttgtcttgaatgtgatatttatggatgataattgaccaaggaagttttgcattatcattctacactgtgcagGTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - aaaaggaa
- - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - -ttgaatg
- - - - - - - - - - - - - - - - - - - - - - - - atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatt