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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtagtttgcccgtatagcattcttattgtcaccttgatcgttctcttggaggaatgagtgatatatctcttatcttaactgatgtcacattgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT

Basic information

species Zea mays
transcript GRMZM2G112609_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 5
ttgtagtttgcccgtatagcattcttattg--tcaccttgatcgttctcttggaggaatgagtgat-atatctcttatcttaactgatgtcacattgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT
 |   || ||   |  |    |  | | ||  | |   |  ||  | |  ||      |    ||  |||||| | ||  | ||  || |    || |||||||||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||| | || ||||| ||||| || || ||||| ||||||||||
attcggtatgaatgcctgatgtattgactgaattaaaattgtcaatatgctgttttcttcttggaccatatctgtaat--tgacaaatattgt-ttctttcagGGTATGATTGCTGGGCATGTGTACTACTTCCTGGAAGATGTATACCCGCGGATGACTGGGAGGCGTCCCCTGAAGACTCCTTCGTTCATCAAGGCGCTAT

upper sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 3'ss of exon 3
ttgta-gtttgcccgtatagcattcttattgtcaccttgatcgt-tctcttggaggaatgagtgatata--tctcttatctt-aactgatgtcacatt---gtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT
  ||| ||||      ||| || | | | |     ||  | | | | | |||  |   |   |     |  | ||| || || |||||| | |  |||   | ||||||||||||||||||| ||||  ||||| || || |||||||| || || || ||||| || ||||| |||||||  || ||    |||||||| ||  | |
--gtatgttttttttcataacaatttcaattaagtctgaaacttgtgttttgctgttgtttatagcccagttttctcatgttgaactgaagacctatttgtggttcagGGTATGATTGCTGGTCATGCCTACTATTTTCTTGAAGATGTGTATCCGCGAATGACAGGTCGTCGGCCCCTAAGAACTCCACAGTTCATTAAAGCAATGT
















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|6601841|gb|AW256282.1|AW256282
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|78124446|gb|DV542830.1|DV542830
EST:     GTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: GTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|76917920|gb|DV167073.1|DV167073
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|91048268|gb|EB158686.1|EB158686
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|211076091|gb|FL368274.1|FL368274
EST:     TTTNGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|50333879|gb|CO529005.1|CO529005
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|56382233|gb|CV984902.1|CV984902
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGA
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|76012317|gb|DT939487.1|DT939487
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
EST: gi|148970116|gb|EE021054.2|EE021054
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTAC
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTAC
EST: gi|60342635|gb|DN209608.1|DN209608
EST:     TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTG                         GGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT
genomic: TTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGT

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: 47 (upstream exon), 47 (downstream exon)
Score: 110

GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 138

GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 137

GTTCTTTTGGGCTTCTCTATCCTCGTTGGAAGCAGCACATGGGTGGACCTCTTGgtatgtttct ... attgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggaggaatgagtgatatatctcttatcttaactgatgtcacattgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT
                                              ttgtttc  CT-rich tract
                          ttatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtagtttgcccgtatagcattcttattgtcaccttgatcgttctcttggaggaatgagtgatatatctcttatcttaactgatgtcacattgtttcagGGTATGATTGCTGGACATGTGTACTACTTCCTGGAAGATGTATACCCACGTATGACTGGGCGTCGCCCCCTAAAGACACCGTCCTTCATTAAGGCGCTAT

- - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt