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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaaaacatttactttttatgtaccttttatgctgccattgctgttctattaacatatattactgtgttcctacctctttcatgtcctatgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT

Basic information

species Zea mays
transcript GRMZM2G119357_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 3'ss of exon 2
----tgtaaaacatttactttttatgtaccttttatgctgccattgctgttctattaacatatattactgtgttcctacctctttcatgtcctatgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT
      || ||       || |  | | | |||||   | |  |   || |  |  ||  | || |  || | |||| |||  || |  ||  |   ||  |||||| ||||| || ||||||   ||||| ||||| |||||||||||||||||||||||||| |||||||| ||| | || ||||| ||| ||||||||| |
tatacatacaaagagatattgtcctttgcattttaaatttctttatatgcttca--aatgt-tacttttg-gctcctgccttatttagatctaactgtatgcagGTTTCATCCTTCATGCATGAGCATGACGATTGAGCAGGCCAAAAAACTAGATCACTTTGTGTGCTCAGATTGTGTCAAGGAAAACGGTGCAAAGAGACCT
















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|20811207|gb|BQ295685.1|BQ295685
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGGCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|211466206|gb|FL385418.1|FL385418
EST:     CATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGA
genomic: CATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTT-GCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGA
EST: gi|29947220|gb|CB816542.1|CB816542
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|87157797|gb|DY402586.1|DY402586
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|87156816|gb|DY401605.1|DY401605
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|89762190|gb|DY689899.1|DY689899
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCCATTGAACAGGCCCAAAAACTAG
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACC-ATTGAACAGGCCAAAAAACTAG
EST: gi|22819298|gb|BU499388.1|BU499388
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|22819350|gb|BU499440.1|BU499440
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAG
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAG
EST: gi|211482256|gb|FL401501.1|FL401501
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|211317910|gb|FL427640.1|FL427640
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|211421418|gb|FL412842.1|FL412842
EST:     CATACAACCCGGATGACCTCATGGTGCAGTGCGAA-CGTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CATACAACCCGGATGACCTCATGGTGCAGTGCGAAGC-TTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
EST: gi|31406109|gb|CD484841.1|CD484841
EST:     CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG                         GTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA
genomic: CCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 147

GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 83

GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 113

GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 101

GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgt ... tgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattaacatatattactgtgttcctacctctttcatgtcctatgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT
   tattaac  putative branch site (score: 101)
     ttaacatatattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaaaacatttactttttatgtaccttttatgctgccattgctgttctattaacatatattactgtgttcctacctctttcatgtcctatgatacacagGTTCCATCCATCTTGCATGGCTATGACCATTGAACAGGCCAAAAAACTAGATCACTTTGTTTGCTCAGACTGTTTGAAAGAAAATGGTTCAAAGAGACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
-gtaaaaca
- - - - - - - - - - - - - - - atgctgc
- - - - - - - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgtg