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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttaacaatgataggcaaaacatgtatttctgtctgtagcatgtgagctaatgtctgtttatgaattatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG

Basic information

species Zea mays
transcript GRMZM2G063792_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 10
gtatgtcttaacaatgataggcaaaacatgtatt-tctgtc-tgtagcatgtgagctaatgtctg-tttatgaattatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG
|||||  ||    || | ||  || ||||  ||  ||| |  |||   ||    |    ||  || |||||   | |||  ||||||||||||||||||||||| || ||  ||| ||| || |||||||  ||||||||||| ||  | | |||||| ||||| |||||  ||||||||| ||
gtatgatttccatatca-agttaatacattcatcgtctattatgtttgatacatgaatctgattgctttattcttcatg--cagAATCTGGTGATGCAAAATGTAGATCATTCTGGGGGCGAGTTCATTGACCTTTTGCAAGGTCTGTTAAGGTATGATCCAGCTAGCCGCCTAACAGCACAAG
















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|211007836|gb|FL013335.1|FL013335
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|37387472|gb|CF630930.1|CF630930
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|40335781|gb|CK369851.1|CK369851
EST:     GAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCATGCTGCGGGAGATTTCATTGGTCTT
genomic: GAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|37385425|gb|CF629852.1|CF629852
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|60358819|gb|DN225792.1|DN225792
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|211519233|gb|FL430929.1|FL430929
EST:     GCACCTCGCGGGAGAGCATGAAACCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|13249792|gb|BG360697.1|BG360697
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|78027627|gb|DV496014.1|DV496014
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|12970020|gb|BG266774.1|BG266774
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|33099166|gb|CF059126.1|CF059126
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|4776116|gb|AI665119.1|AI665119
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
EST: gi|16378565|gb|BI992494.1|BI992494
EST:     GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAG                         AATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT
genomic: GCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTT

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), 48 (downstream exon)
Score: 161

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 196

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 180

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 141

GCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACCTCGCGGGAGAGCATGAAAGCTGTGATGAAATTGTCCAGGCTTCAGgtatgtctta ... ttatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtatttctgtctgtagcatgtgagctaatgtctgtttatgaattatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG
                         agctaat  putative branch site (score: 141)
                                     tttatgaattatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttaacaatgataggcaaaacatgtatttctgtctgtagcatgtgagctaatgtctgtttatgaattatgaacagAATCTGGTGATGCAAAATGTGGACCAGGCTGCGGGAGATTTCATTGGTCTTTTGCAAGGGCTCCTGAAGTATGACCCAGCAAGCCGTTTAACAGCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG