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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttctacgtggtatgctaacattatatacttctagcattcatctgaccttggaagaatgatttggaatatttgaccatgttgttcatgcaccattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA

Basic information

species Zea mays
transcript GRMZM2G006781_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g35290.1 (Oryza sativa), 3'ss of exon 2
ctttctacgtggtatgctaacattatatacttctagcattcatctgaccttgg-aagaatgatttggaa--tatttgaccatgttgttcatgcacc-attgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA
   |||| |||  |||| |   ||||  | ||   |  |||     |   ||| | | |  |||||     | ||||  ||  |||| |||  |   |||  |||||||||||||||| || ||||||||||||||||| ||||||||||| || ||||| |||||||| || ||||||||||| ||||| |||||||||||||
--gtcta-gtgagatgc-atttttatgcaatttaggttttctcagcagtatggcatgtaatatttgacccttttttgtgcactttgtacatttatttattacagATAGAGGAGATACCGAATTTAACATCTGGCTGCACCGAGTTTGTTGAGTCAGCACAGCAAATTTTAGAAGAGAGGAAGCTCAATCAGACATTACTAGCCA

upper sequence: GRMZM2G006781_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 2
ctttctacgtggtatgctaacattatatacttctagcatt---catctgaccttggaagaatg-atttgga--atatttgaccatg-ttgttcatgcaccattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA
      ||    | || | |  |  ||   ||| |  | |    || | | | |||||||||  |  | ||  | || | |   || || ||      ||  || ||||| | || ||||||||  | |||||||| |||||||||||  |||| || ||| |||| |||||||||||||| ||| | || |||||||| |||||||
------actgaatttgatcatgtc-tacctttccaatactatctatataagcatggaagaatttaagtagatcagatataatggtgatttttttctttcctctgcagATAAATGAAATACCAAAGCTGACATCTGGTTGCACTGAGTTCATTGAGTCTGCAGAACAGATTTTGGAGGAGAGAAAGATGAACCAAACATTGCTAGCCA
















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|149008084|gb|EE040323.2|EE040323
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|148939698|gb|EC884368.2|EC884368
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|148979834|gb|EE026851.2|EE026851
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|4730483|gb|AI649649.1|AI649649
EST:     CAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|71305530|gb|DR788908.1|DR788908
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|211334830|gb|FL416303.1|FL416303
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|148986186|gb|EE029955.2|EE029955
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|71316958|gb|DR795163.1|DR795163
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|211423964|gb|FL408859.1|FL408859
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGTGATACCAAACTTAACATCTGGCTGCCCTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|86469576|gb|DY235946.1|DY235946
EST:     CCTTCGTCCGCGCGCATCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGATTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|148963434|gb|EE014450.2|EE014450
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|148999331|gb|EE036267.2|EE036267
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|211082178|gb|FL396889.1|FL396889
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCNAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
EST: gi|71449856|gb|DR830906.1|DR830906
EST:     CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATG                         ATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC
genomic: CCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCC

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: 46 (upstream exon), 48 (downstream exon)
Score: 84

GGTGGCGGTGGAAAACTACGCCGCGTTCATCGCCGCCTCTGAGGCGCTCTCCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 47

GGTGGCGGTGGAAAACTACGCCGCGTTCATCGCCGCCTCTGAGGCGCTCTCCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA


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

GGTGGCGGTGGAAAACTACGCCGCGTTCATCGCCGCCTCTGAGGCGCTCTCCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

GGTGGCGGTGGAAAACTACGCCGCGTTCATCGCCGCCTCTGAGGCGCTCTCCTTCGTCCGCGCGCAGCTTGAGAGCTTCGACGGCCACCTCGAGGCCATGgtaatgcggc ... accattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccttggaagaatgatttggaatatttgaccatgttgttcatgcaccattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA
                     aatatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttctacgtggtatgctaacattatatacttctagcattcatctgaccttggaagaatgatttggaatatttgaccatgttgttcatgcaccattgtagATAGAGGAGATACCAAACTTAACATCTGGCTGCACTGAGTTTGTTGAATCCGCACAACAAATTTTGGAGGAGAGGAAGCTTAATCAAACATTACTAGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - -gtatgct
- - - - - - - - - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcatgc