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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagattccttacatgtgaagtttctgattcggaatattttctgacctcttgctaaaataagaacttggctggtatttttcaacctactgctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG

Basic information

species Zea mays
transcript GRMZM2G111510_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111510_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g53560.1 (Oryza sativa), 3'ss of exon 9
actagattccttacatgtgaagtttctgattcggaatattttctg----acctcttgctaaaat----aagaacttggctggtatttttcaacctactgctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG
       |  |||||  ||| |||  |||| |   |||||  ||     || | ||| |    |    |||||       | ||   | ||||||||| |  || ||| |||||||||||| |||||||||||| | || |||| |||||||||||  ||||||  |||||| ||||||| || ||  ||
-------ttgttacacatga-gttcatgatgcacgatattacctcttatacatgttgttgctttttttaagaatgcaatcgttaagctccaacctacttcaagtgcagTGTTGGTGCAGACAAGTGGTCTTTACTGTATGAATCGATTCCAGAAAAGCTGCAAATCCTGTACAATGATGGCTATAAATTG
















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|166431997|gb|EG103175.1|EG103175
EST:     ACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|78088731|gb|DV517124.1|DV517124
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|60359551|gb|DN226524.1|DN226524
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|71432125|gb|DR813175.1|DR813175
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|60341580|gb|DN208553.1|DN208553
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|211443974|gb|FL182596.1|FL182596
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|60336621|gb|DN203594.1|DN203594
EST:     TTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: TTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|91053260|gb|EB163678.1|EB163678
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTGGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|71316663|gb|DR795006.1|DR795006
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|60342489|gb|DN209462.1|DN209462
EST:     CCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: CCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|60401163|gb|DN233970.1|DN233970
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|32932991|gb|CF037803.1|CF037803
EST:     ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAG                         GGTTGGTGCAGACCAGTGGCCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: ATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
EST: gi|60351350|gb|DN218323.1|DN218323
EST:     CAGTATGAAGAG                         GGTGGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT
genomic: CAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATT

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: 229

GAAGATGGCCTTCATGCTTCATCTAAGATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

GAAGATGGCCTTCATGCTTCATCTAAGATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

GAAGATGGCCTTCATGCTTCATCTAAGATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 54

GAAGATGGCCTTCATGCTTCATCTAAGATTGCTGCATTTGATTTTGATGGGTGCCTTGCCAATACCAGTATGAAGAGgtattgtgtt ... gctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctcttgctaaaataagaacttggctggtatttttcaacctactgctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG
      tgctaaa  putative branch site (score: 54)
                                              ctcgtcc  putative PPT
         taaaataagaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagattccttacatgtgaagtttctgattcggaatattttctgacctcttgctaaaataagaacttggctggtatttttcaacctactgctcgtccagGGTTGGTGCAGACCAGTGGTCTTTACAGCATAAATCAATTCCAGAAAAATTGCAAAGACTGTACGATGATGGTTACAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - -catgtga
- - - - - - - - - - - tttctga
- - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggctggt