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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtcgtttctatgatcaatatcaatgatgttacctttttttatccttttggtgctagtatttatcatctttactgaaatgagttgtcctaatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA

Basic information

species Zea mays
transcript GRMZM2G017086_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 4
cttgtcgtttctatgatcaatatcaatgatgttacctttttttatccttttggtgctagtatttatcatctttactg-aaatgagttgtcct----aatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA
       |   || || |  ||| |   || |  | |     | |   | |  |  | || ||  | |||| | ||| || |||| | ||       |  || |||| ||||||||||||||||||||| | ||||||||||| || ||||||||||| ||||| || |||||||||||||||||||||||||||||  |  | |
---aaattgcttaagagcgctattat--atttggcataagcatgttggtcttattttggtgttcttaatctgtgctgcaagtgagatttctctttggaatttcagGGACACAGTGCTGGTCTTTATAACTTGGGGAATACATGTTACATGAATTCCACTTTGCAGTGCCTGCATTCTGTTCCAGAGCTGAAGTCAGCTTTATTGA

upper sequence: GRMZM2G017086_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G01480.1 (Glycine max), 3'ss of exon 4
-------cttgtcgtttctatgatca-atatcaatgatgttacctttttttatccttttggtgctagtatttatcatctttactgaaatgagttgtcctaatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA
       ||  | |  |   |  |   || ||| ||||             ||  ||||| |  ||| ||||    | |||  |    |  ||| |||||       ||| || | |||||||||||  ||| | || || ||||| ||||||||||| ||||||||||| || |||||||| || ||| | ||||||||  ||   |
attaattctcattgaatgactagttttatctcattgataactagagaaggaatatttttg-ttttagcatttgattttttttttcctgttggttttccta-------gGGGCATACTGCTGGTCTTTTCAACTTGGGAAACACATGTTATATGAATTCAACATTGCAATGCCTCCATTCTGTGCCTGAGTTAAAGTCAGCTTTGACTA
















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|211321831|gb|FL416221.1|FL416221
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|211354449|gb|FK991826.1|FK991826
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|211085323|gb|FL409653.1|FL409653
EST:     TCCAGTGTTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: TCCAGTGTTT-GTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|211354448|gb|FK991825.1|FK991825
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGAATGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|241994792|gb|GR421145.1|GR421145
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|211536230|gb|FL396283.1|FL396283
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|32935100|gb|CF039912.1|CF039912
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|31998167|gb|CD661962.1|CD661962
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|13237239|gb|BG355253.1|BG355253
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
EST: gi|33094903|gb|CF054897.1|CF054897
EST:     GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTG                         GGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC
genomic: GTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCC

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: 210

GTTGATGATGATAGGCACGGCTGATGAGATTGTGAAAGCTCCGGAGAAAGGTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 185

GTTGATGATGATAGGCACGGCTGATGAGATTGTGAAAGCTCCGGAGAAAGGTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTTGATGATGATAGGCACGGCTGATGAGATTGTGAAAGCTCCGGAGAAAGGTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

GTTGATGATGATAGGCACGGCTGATGAGATTGTGAAAGCTCCGGAGAAAGGTCCAGTGTTTGTTGAGGATCTACCAGAAGAAGAGCAAGTGATTGCACTGgtacatacca ... taatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttggtgctagtatttatcatctttactgaaatgagttgtcctaatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA
                                          tcctaat  putative branch site (score: 232)
                                       ttgtcct  CT-rich tract
              tatttatcatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtcgtttctatgatcaatatcaatgatgttacctttttttatccttttggtgctagtatttatcatctttactgaaatgagttgtcctaatatttagGGTCACAGTGCTGGTCTTTATAACCTTGGGAATACATGCTATATGAATTCCACATTGCAATGTCTGCATTCTGTTCCAGAGCTGAAGTCAGCGCTGCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -ggtgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaatg