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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaattcgagaagacaaattgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT

Basic information

species Zea mays
transcript GRMZM2G171781_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 2
gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaatt-cgagaagacaaattgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT
                                        | | |||  |    ||  || |   |||   |   || | |    |||| |||     || |   |        |  |   |  || ||   |  || |||   |||||||| |     |   ||||||||||||||| ||||| ||||| ||||| || ||||||||||||||||||||||||||||| |||||||||||||| |||||| | || || ||||||||||||||
---------------------------------------gtgagctcaaacaagtcttctgcatttcctcgt---ttataccagcttccgattcttctcttatctcttctccaacaattctactcc-ctgaattggtccaaaattctaaatttcttcctggtgaattgttgcagGGCTCCAAAGATGCGGCAAGAGCTGCAGGCTGAGGTGGATAAACTATCTGAGGCCTGACCTCAAGAGAGGTGCATTCTCTCAGGAGGAAGAAGACCTCAT

upper sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G26660.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaattcgagaagacaaattgttg--cagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT
                                                            | |  || || ||   | || | |||    || ||     ||      | | |  ||    |||    |            |||| |   || | | | | | ||  |     |||  | ||||| || |||||||||||||| || ||||||||||| ||| |||| |||||  | |||||||| || ||| | ||||||||||||  | | ||
-----------------------------------------------------------gtttggtctctatgtgctcttat-attatatatagcttaaagaggtttatatagcatcgtttataatgttt-----------ttatatgcgttggtggatatatatgatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGAGACCAGATTTAAAGAGAGGAGCTTTCTCTCAAGACGAAGAAAGCTTGAT

upper sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S189_29V6.1 (Physcomitrella patens), 3'ss of exon 1
gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaattcgagaagacaaattgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT
                                                           | ||| |  ||||  |        | |||  ||  || | ||| |||  | | |  |   |  |   || | | |  |    |   ||  |         ||||       ||||| | || || || ||||| || || ||| | ||||||||||||||||||||||||||| | ||| ||||||  ||| | | ||  || ||  | || ||
---------------------------------------------------------tttcctctttgctctaaaaaaagaaaagttcagataccccgttgacaccaatttagaataagagttgtgtcgctgacgctggtgtgccctgga---------acaa-------cagGGTTACAGAGATGTGGAAAAAGCTGCAGGTTAAGGTGGATAAACTATCTGAGGCCAGACTTAAAGCGAGGGGTTTTCTCACCAGCAGAGGAGAATCTGAT

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|93016059|gb|EB641579.1|EB641579
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|89756257|gb|DY686346.1|DY686346
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|71428058|gb|DR809108.1|DR809108
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|211542127|gb|FL161867.1|FL161867
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAA-GGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|71306951|gb|DR789632.1|DR789632
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|211542123|gb|FL161863.1|FL161863
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|211542121|gb|FL161861.1|FL161861
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|211542122|gb|FL161862.1|FL161862
EST:     ATAACAAAGCATGGCCATGGGCTGCTGGAGCTCTGTTCCCAAACTCCCTG                         GGCTTCAAAGGTGCGGAAAGAG
genomic: ATAACAAAGCATGGCCATGG-CTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAG
EST: gi|89251317|gb|DY623103.1|DY623103
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
EST: gi|89762273|gb|DY689946.1|DY689946
EST:     CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTG                         GGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA
genomic: CATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGA

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: 45 (upstream exon), 40 (downstream exon)
Score: 16

CTGAGAAAGGGGCTCTGGTCCCCTGAGGAGGATGAGAAACTCATGAATCACATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 63

CTGAGAAAGGGGCTCTGGTCCCCTGAGGAGGATGAGAAACTCATGAATCACATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT


Block sizes: 29 (upstream exon), 46 (downstream exon)
Score: 9

CTGAGAAAGGGGCTCTGGTCCCCTGAGGAGGATGAGAAACTCATGAATCACATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT


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

CTGAGAAAGGGGCTCTGGTCCCCTGAGGAGGATGAGAAACTCATGAATCACATAACAAAGCATGGCCATGGCTGCTGGAGCTCTGTTCCCAAACTCGCTGgtatgtacga ... attgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatacctctcggtcagttcaattatctaaattcgagaagacaaattgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT
                         atctaaa  putative branch site (score: 44)
                  ttcaattatctaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaattcgagaagacaaattgttgcagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG