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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcctttttttttgcatatcgacttttgcctgctttgttctagataaatcgttgcatatttttcatgtcatcctttgatttggtttgccaaacat...

Basic information

species Zea mays
transcript GRMZM2G056975_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os01g01710.1 (Oryza sativa), 5'ss of exon 11
CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcctttttttttgcatatcgacttttgcctgctttgttctagataa-atcgttgcatatttttcatgtcatcctttgatttggtttgccaaacat-
| ||||| || ||||||||||||||  | ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| || || ||||||||  ||  |  |   |   |   || || ||   |   |  | |||   |||||   || || || | | || |  ||   |    ||   ||  |  
CGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTTCTGAGTGCTGCTAATGAGAAGGCTGTGGAGTTGTTCATCGATGAAAAgtatgacactcatcatcatcccttttcctctttcc-attgcatagtggattccatcgtctgattttgtttacg-cacctattctctgcaattttaaaggaga

upper sequence: GRMZM2G056975_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA17G09740.1 (Glycine max), 5'ss of exon 11
CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct---ttttttttgcatatcgacttttgcctgctttgttctagataa-atcgttgcatatttt-tcatgtcatcctttgatttggtttgccaaacat-----------------------------------------------------------------------------------
| ||| | || |||||||| |||||||| ||||| ||||| |||||||||||||| || || || |||||||| || || ||| |||| ||||| || ||||| | |  |   ||||||||   | |  | |            | | |||||    || |  |||  |   |  |  |||  ||  | |    ||  | ||                                                                                      
CCATGAATCTTGCCTATGCTGCTGGCCGTGCTGGAGGCACAATGACAGGAGTTCTTAGTGCAGCAAATGAGAAAGCTGTAGAGATGTTTATTGATGAAAAgtaagtttttagtttttttttttttctaaattacaaataagaaagctgtagattgtgtcatgtcattctaagttctaacatttttgaagtgtccttatccaatggctttatagatcatagggtacatcatacatgtgtcttattgtcaacgtaaattctcctctaattggctattttgctgcttccag

upper sequence: GRMZM2G056975_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 5'ss of exon 11
CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcctttttttttgcatatcgacttttgcctgctttgttctagataaatcgttgcatatttttcatgtcatcctttgatttggtttgccaaacat
| ||||| || |||||||| ||||| |||||||| |||||||||||||||||||| || || |||||||||||||| |||||| |||| ||||| || |||||||    | ||    | | |       |    |    |||   ||  ||   |    ||            |     |  ||||  | |   |  | |
CCATGGATCTTGCCTATGCTGCTGGACGGGCTGGAGGCACCATGACAGGAGTTCTTAGTGCAGCTAATGAGAAGGCTGTGGAGATGTTTATTGATGAAAAgtatgtaattattccagtccttgctaggctcccaccttattgggatacttattccacatcaggaccagggaaccgaaaatgcatttattgttttatgctt

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|16379495|gb|BI992983.1|BI992983
EST:     GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|14244555|gb|BG840684.2|BG840684
EST:     GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|31362671|gb|CD447028.1|CD447028
EST:     GTCCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|67032629|gb|CO461378.1|CO461378
EST:     GTCCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|37421752|gb|CF648577.1|CF648577
EST:     AATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: AATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|6601843|gb|AW256284.1|AW256284
EST:     GTCCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|84970217|gb|DW468567.1|DW468567
EST:     GTTTTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|18167286|gb|BM337125.1|BM337125
EST:     GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|71445034|gb|DR826084.1|DR826084
EST:     GTTTTGAGCGCTGTTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|89252718|gb|DY624504.1|DY624504
EST:     GTTTTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGGGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|86474441|gb|DY240811.1|DY240811
EST:     GTTTTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|71596069|gb|DR906820.1|DR906820
EST:     GTCCTGAGCGCTGCTGATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|12968309|gb|BG265255.1|BG265255
EST:     GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|16377664|gb|BI992045.1|BI992045
EST:     GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
EST: gi|211274635|gb|FL463120.1|FL463120
EST:     GTCCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAA                         GATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA
genomic: GTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCA

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: 65

CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCATCGGAACGAGCTGGTAACAAGCCCGTCACTGGAGGAGATCGTCCATTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 834

CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCATCGGAACGAGCTGGTAACAAGCCCGTCACTGGAGGAGATCGTCCATTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 583

CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCATCGGAACGAGCTGGTAACAAGCCCGTCACTGGAGGAGATCGTCCATTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcct ... ggttttgcagGATTAGCTACCTGGACATATTCAAGGTGGTGGAGCTTACATGTAACGCGCATCGGAACGAGCTGGTAACAAGCCCGTCACTGGAGGAGATCGTCCATTAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTTCTGAGCGCTGCTAATGAGAAGGCCGTGGAGTTGTTCATTGACGAGAAgtatgatcctttttttttgcatatcgacttttgcctgctttgttctagataaatcgttgcatatttttcatgtcatcctttgatttggtttgccaaacat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG