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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatacctgatttctgtggaattattacgacaagttcagcttttttgcctgaccatgtcaaccatctctgaccctgtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC

Basic information

species Zea mays
transcript GRMZM2G020553_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020553_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g27220.2 (Oryza sativa), 3'ss of exon 4
-gtaagatac-ctgatttctgtggaattattacgacaagttcagcttttttgcctgacca------tgtcaaccatctctg---accctgtgt-tctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC
  |||  |    || |||  |     | |||   |    |||     | |   |  | ||      | | |||||||        |  | | | |||||| || ||||||||| |||||||||| ||||||||| |||| ||||||   |||| |||||| || ||||||||||||||| | | ||| |||||||| |||
attaaattgtgttggtttgagccttttgattttaaagcattccatggtataaacaaaacaactgaatataaaccatcctgatgtgcattatttgtctcagAATTCAAAGGTGGTTCTTCCCCTATGACTACCAAGTAATCCAGGAGATGCACAGGGATGAACCCCACGAGTACAGCAGGATACAACTTCCAGAGACAAGC
















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|67034835|gb|CO463368.1|CO463368
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
EST: gi|213170626|gb|FM190014.1|FM190014
EST:     ATCGTACTTGTTCCGATCATNGCCCTGTTTGGGGATTTCCTATATCTATN                         NATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAAATACAGGAGCA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAA-TACAGGAGCA
EST: gi|211218457|gb|FL333870.1|FL333870
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
EST: gi|211161907|gb|FL325524.1|FL325524
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
EST: gi|211187926|gb|FL314078.1|FL314078
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
EST: gi|211201168|gb|FL362526.1|FL362526
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
EST: gi|211083687|gb|FL340069.1|FL340069
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
EST: gi|67022255|gb|CO451004.1|CO451004
EST:     ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATC                         GATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA
genomic: ATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACA

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: 48 (upstream exon), 48 (downstream exon)
Score: 92

TGTATTTTGTGATTTATGTTCTGATGAGCACCTTTTTCTTCTATCTGACAATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 65

TGTATTTTGTGATTTATGTTCTGATGAGCACCTTTTTCTTCTATCTGACAATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

TGTATTTTGTGATTTATGTTCTGATGAGCACCTTTTTCTTCTATCTGACAATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 80

TGTATTTTGTGATTTATGTTCTGATGAGCACCTTTTTCTTCTATCTGACAATCGTACTTGTTCCGATCATCGCCCTGTTTGGGGATTTCCTATATCTATCgtaagatacc ... gtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttcagcttttttgcctgaccatgtcaaccatctctgaccctgtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC
                                   ctctgac  putative branch site (score: 80)
                                              tgttctc  putative PPT
          tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatacctgatttctgtggaattattacgacaagttcagcttttttgcctgaccatgtcaaccatctctgaccctgtgttctcagGATCCAAAGGTGGCTCTTCCCCTACGACTACCAAATAATACAGGAGCAACACAAGGATGAGCCACACGAGTACAGCAGGGTGCCACTACCAGAGACCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG