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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccatttcaagtcagttcctcactgcattgataagcatctttatgctgactttctgtgtgtaccttttgctgttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG

Basic information

species Zea mays
transcript GRMZM2G138886_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138886_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g47580.1 (Oryza sativa), 3'ss of exon 9
-------------------------------gtaagtccatttcaagtcagttcctcactgcattgataagcatctttatgctgactttctgtgtgtaccttttgctgttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG
                                |  ||  |     | | |  || |||      || | | |||  ||  |||||  |  | | | |  || ||| | | ||   ||| ||||| || ||||||||||||||||| ||||||||||| ||| |  | |||||||| ||||||||| |||| |||||||| | |||||| || || |  
gtaagtagcacttcgccttcgcattccctgcctgcgtttacaagcatttatgtcttcagatgtatggtgatcatacttgagctga--tcatatttctttctcttgttctccttttcagTGAGTGTTCTAGGATGATGGTAGATTTCCACCAGAAGGCGGGAGCAGGCAAGCTCACCGGCGTGCACCGGAAATACAGTACGTTCAAGTTTGGGTGTGCA
















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|78124436|gb|DV542820.1|DV542820
EST:     TGGACAAAGGTTTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|71760161|gb|DR958098.1|DR958098
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|9951959|gb|BE638542.1|BE638542
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|12973190|gb|BG268357.1|BG268357
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|76015405|gb|DT942575.1|DT942575
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|50324449|gb|CO519575.1|CO519575
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|76283025|gb|DV022593.1|DV022593
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|211247236|gb|FL156676.1|FL156676
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|211420117|gb|FL461558.1|FL461558
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|76015404|gb|DT942574.1|DT942574
EST:     TGGACAAAGGTTTGCGAGTTTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|6601796|gb|AW256237.1|AW256237
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|30307156|gb|CD001829.1|CD001829
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
EST: gi|71418564|gb|DR804478.1|DR804478
EST:     TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCT                         GGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA
genomic: TGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAA

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: 247

CTGCTGCTGCGGTTTATACTGCACAGTGTGCTATCAATCGTTGCCAGCACTGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 9

CTGCTGCTGCGGTTTATACTGCACAGTGTGCTATCAATCGTTGCCAGCACTGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 12

CTGCTGCTGCGGTTTATACTGCACAGTGTGCTATCAATCGTTGCCAGCACTGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 15

CTGCTGCTGCGGTTTATACTGCACAGTGTGCTATCAATCGTTGCCAGCACTGGACAAAGGTCTGCGAGTCTCATAGCAGATACACTAGCGACCAACTCCTgtaagtccat ... ttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgataagcatctttatgctgactttctgtgtgtaccttttgctgttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG
                tgctgac  putative branch site (score: 15)
                                   ccttttgctgttctc  putative PPT
         atctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccatttcaagtcagttcctcactgcattgataagcatctttatgctgactttctgtgtgtaccttttgctgttctcaccagGGAGTGCTCGAGGATGATGGTAGATTTTCACCAGAAGGCTGGAACCAGTAAGCTCACTGGCGTGCACAGGAAGTACAGTACCTACAAGTTCGGTTGCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA