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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactaatgtttaatattgtgtagagaagttgcatgatagactttgcaatgcctaagttaaacattgcaatagaaacatgcatcgcatgcgattaattagcacttgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA

Basic information

species Zea mays
transcript GRMZM2G091245_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091245_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g25700.1 (Oryza sativa), 3'ss of exon 5
--------gtaagcactaatgtttaatattgtgtagagaagttgcatgatagactttgcaa--tgcctaagttaaacattgcaatagaaacatgcatcgcatgc----gattaattagcacttgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA
            || || ||  | | | |||||||||||| |  |||||  ||| | | |   | |||||    || ||  |||   | |||||||| | |||     | | |||||  | |||  | ||||||||||||| || |||||||||||  | ||||| || ||||||||||| || ||| |||||||| | ||| | |||||||| |||||  |||| | ||||
gtacggacacttgccctgatactcact-ttgtgtagagaactgtcatgaatgacatcgtaccttacctaatacgaaaataccaa---acacatgcattggatgacctgggtgaattattatttggctgacagGAAAAATGGCTCTTGGCTTCTGCCCTTGGCACTTATCCCTTTTGTGGGACCTTCATTGTATCTTTTGCTGAGGCCATCACTCTCTTCTCTGCTAGCAGCA
















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|32840714|gb|CD980395.1|CD980395
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|78122779|gb|DV541163.1|DV541163
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|32840712|gb|CD980393.1|CD980393
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|110936902|gb|EE157059.1|EE157059
EST:     TCAGCCTTCTCACCATTTTGGGTTTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|78112130|gb|DV530526.1|DV530526
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|60345247|gb|DN212220.1|DN212220
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|32840815|gb|CD980496.1|CD980496
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
EST: gi|211227758|gb|FL051794.1|FL051794
EST:     TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATG                         GAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC
genomic: TCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCC

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: 12

ATCCATGCCACCTGCCTTGATTTTACTTTGCTATCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67

ATCCATGCCACCTGCCTTGATTTTACTTTGCTATCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24

ATCCATGCCACCTGCCTTGATTTTACTTTGCTATCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 36

ATCCATGCCACCTGCCTTGATTTTACTTTGCTATCAGCCTTCTCACCATTTTGGGTCTATAACGACATGACAGCAAGGCGATGgtaagcacta ... tgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacattgcaatagaaacatgcatcgcatgcgattaattagcacttgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA
                               gattaat  putative branch site (score: 36)
                                           cttgctt  putative PPT
                                attaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactaatgtttaatattgtgtagagaagttgcatgatagactttgcaatgcctaagttaaacattgcaatagaaacatgcatcgcatgcgattaattagcacttgcttaacagGAAAAATGGTTCATGGCTTCTGCCGCTTGCACTGATACCTTTTGTGGGGCCCTCACTGTATCTTCTACTGCGCCCATCACTTTCTTCCTTGCTGGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG