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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggagaccgtcgtcaactgagttcatcgagtgctatggtgaccccccccccccctgttaacttaatgctgacatggttcacgtgacattaaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA

Basic information

species Zea mays
transcript GRMZM2G143356_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 2
---taggagaccgtcgtcaactgagttcatcgagtgctatggtgaccccccccccccctgttaacttaatgctgaca--tggttcacgtgacattaaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA
   | | ||||  ||    | | |||  || |  |  | |  |||    | |      || || || | | ||   |  || ||        |  |||||||||||||||||| || || ||||||||||||||||| |  |||||||||||||| ||||| |||||||||||
caattgaagactatc--tgatttagtcaataggtttttcttatgatgatctcttat--tgcta-ctcagtacttgtaactgatttctactttaccaaaattgcagGGATTGGTCTTCCTATTCAGCATGCTAGGAATAACACCTTTAGCTGAGCGCTTGGGTTATGCAACTGA
















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|148951918|gb|EC897694.2|EC897694
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|211103676|gb|FL335622.1|FL335622
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCCTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|211203502|gb|FL354146.1|FL354146
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|148952030|gb|EC897816.2|EC897816
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|149080754|gb|EE169818.2|EE169818
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|211283838|gb|FL366656.1|FL366656
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTT
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTT
EST: gi|211019237|gb|FL365611.1|FL365611
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|149075868|gb|EE164419.2|EE164419
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
EST: gi|211078111|gb|FL332550.1|FL332550
EST:     TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACAT                         GGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA
genomic: TGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGA

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: 47 (upstream exon), 48 (downstream exon)
Score: 32

GCTCAGGAGCATCAGGATCGTCATTTTTACTTCCAAGCTCAACTTGCTCATGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA


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

GCTCAGGAGCATCAGGATCGTCATTTTTACTTCCAAGCTCAACTTGCTCATGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

GCTCAGGAGCATCAGGATCGTCATTTTTACTTCCAAGCTCAACTTGCTCATGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

GCTCAGGAGCATCAGGATCGTCATTTTTACTTCCAAGCTCAACTTGCTCATGCCGTTCGGACCTGCCTCCATCATTCTCCACTTCACGACTAGGAGACATgtaagtgctg ... aaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccccccccctgttaacttaatgctgacatggttcacgtgacattaaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA
                     tgctgac  putative branch site (score: 112)
                                        acattaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggagaccgtcgtcaactgagttcatcgagtgctatggtgaccccccccccccctgttaacttaatgctgacatggttcacgtgacattaaaattgcagGGATTGGTTTTTCTTTTCAGCATGCTAGGAATTATGCCTTTAGCTGAGCGATTGGGATATGCAACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - -gttcatc
- - - - - - - - - - - - - - - -tgctatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacatt