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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctaccgtacacaataaatctttgaatcatcattattggttctgcataattttaactgctaatcctagacttattttatgcatcacttcatctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG

Basic information

species Zea mays
transcript GRMZM2G089484_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 9
---------------tatctaccgtacacaataaatctttgaatcatcattattggttctgcataattttaactgc-taatcctagacttattttatgcatcacttcatctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCG---ATATGAGCAACGAAGAATCGCTAG
               || |    |     ||       || ||     ||  |   || |   |    |  | ||  | |  | |||   |||||   | | || | ||||  |||||| || |||||| |||||||||||||||||||||||| |||  ||| |    ||| |  |  | ||||| ||||    ||||||||| |||||  | |    
gttagcatctgtccttaccagttgactttaacctgcaattaaacttgtatcctccattatatctttcatacattgtgtgactcaagatagattttgcacgttacct-atcttccagGTGCTGCTGCAAGACCTGGTAAAGCAGTTGGTTCGGTGCTGCGTTACGGTAACTGTTCGACATCCGCTGCTGAGCAACAATATGAGCAGCGAAGGGTTGT---
















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|60397061|gb|DN229880.1|DN229880
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|14245174|gb|BG873756.1|BG873756
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|32835922|gb|CD975600.1|CD975600
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGT
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGT
EST: gi|211150023|gb|FL261061.1|FL261061
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|32835600|gb|CD975278.1|CD975278
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTAC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTAC
EST: gi|6020557|gb|AW065590.1|AW065590
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGNTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|5860478|gb|AW011700.1|AW011700
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|9742629|gb|BE518777.1|BE518777
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCGCCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|60351950|gb|DN218923.1|DN218923
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|32835454|gb|CD975132.1|CD975132
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTAC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTAC
EST: gi|32862753|gb|CF002435.1|CF002435
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|69351561|gb|DR452176.1|DR452176
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|32833224|gb|CD972902.1|CD972902
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGT
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGT
EST: gi|37381934|gb|CF627875.1|CF627875
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATTCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|71763203|gb|DR961140.1|DR961140
EST:     TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|9742842|gb|BE518990.1|BE518990
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTCGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
EST: gi|5847343|gb|AW000422.1|AW000422
EST:     TCCATATCCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAG                         GTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC
genomic: TCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCC

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: 190

ACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACATCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

ACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACATCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

ACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACATCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

ACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACATCCATATTCTGCTTCTGTTGCAAGTAAATTTCCACCACATGTTCCTCAAGgtaaacacct ... catctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcataattttaactgctaatcctagacttattttatgcatcacttcatctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG
             tgctaat  putative branch site (score: 86)
                                          cttcatct  putative PPT
                      tagacttattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctaccgtacacaataaatctttgaatcatcattattggttctgcataattttaactgctaatcctagacttattttatgcatcacttcatctgacagGTGATGTTGCAAGGCCTGGTAAAGCAGTTGGTTCGGTGATGCAGTACAGCCCATGTCCAGCGCCTGCTGCCGAGCGATATGAGCAACGAAGAATCGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - -caataaa
- - - - - - - - - - - - - - - - - - - - gttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatc