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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttcttgcttcagagttatgcttgcaacctttttagcttaacctgaatcattccaatggctttactgtcag

Basic information

species Zea mays
transcript GRMZM2G484880_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g34305.1 (Oryza sativa), 5'ss of exon 10
TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgc-----tttcttg-cttcagagttatgctt-------gcaacctttttagcttaacctgaatcattccaatggctttactgtcag------------
| |||||||| ||||||||||| |||||||| ||||| ||||||||  | ||||| ||||||| |||| |||||||| |||||||||| ||     |||||||  || |  ||| | | |       ||| | | || |  |       |   |  | |||   | |   |||||            
TGAAATTGCCGGAGCTACTTGCGTCTGTCAACATGGAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaatctttcttgattttattgttgtacatcactatagcagcatattcatttcccatcaatatacacaaata--tgtgaagtcagttagcaccttca

upper sequence: GRMZM2G484880_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g01130.1 (Oryza sativa), 5'ss of exon 10
TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgc-----tttcttgcttc-------agagttatgcttgcaacctttttagcttaacctgaatcattccaatggcttta--ctgtcag---------
| |||||||| ||||||||||| ||||| || ||||| ||||||||  | ||||| ||||||| |||| |||||||| |||||||||| ||     ||||||| ||         | || |   | ||||| | || |  |       |   |  | |||   |  |  | || ||         
TGAAATTGCCGGAGCTACTTGCGTCTGTTAACATGGAAGAAGATGCACTCAACAAACTACAGCAGAAATTGCTGGACATTCTCAAgtaagcaaatatttcttgattttattgttggcgtcactatggcaacatattcatttcccatcaatatacacaaatatgtgaagtcggttagcaccttcat
















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|5762213|gb|AI967261.1|AI967261
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|166684871|gb|EG164435.1|EG164435
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAG
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAG
EST: gi|22546503|gb|BU098814.1|BU098814
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|211181083|gb|FL441231.1|FL441231
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|93284202|gb|EB676466.1|EB676466
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|31997933|gb|CD661838.1|CD661838
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|60358481|gb|DN225454.1|DN225454
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         --------A-A-GAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|60343282|gb|DN210255.1|DN210255
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|37386752|gb|CF630565.1|CF630565
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|211165206|gb|FL438738.1|FL438738
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|20208496|gb|BQ134585.1|BQ134585
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|33103032|gb|CF062992.1|CF062992
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         ATTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|6020484|gb|AW065412.1|AW065412
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTGCGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|32866884|gb|CF006566.1|CF006566
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|211399030|gb|FL440153.1|FL440153
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|76016791|gb|DT943961.1|DT943961
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|78544095|gb|DV621593.1|DV621593
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|22546502|gb|BU098813.1|BU098813
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCCCCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|9952124|gb|BE638722.1|BE638722
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|71759434|gb|DR957371.1|DR957371
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|32937879|gb|CF042698.1|CF042698
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     AGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTTCTCA-                         GTTTCTTCAGAAGAATCAGATCACCTTC
genomic: AGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTT-CTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTC
EST: gi|8666010|gb|BE186826.1|BE186826
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|211058553|gb|FK994418.1|FK994418
EST:     GAGGAAGATSCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
EST: gi|5917408|gb|AW054199.1|AW054199
EST:     GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAA                         GTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC
genomic: GAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTC

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: 48 (upstream exon), 47 (downstream exon)
Score: 210

TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTCTTGTAAAGGTGCAGATGAGGATAAAACCAAATGATTGCATGTGAACGTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTCTTGTAAAGGTGCAGATGAGGATAAAACCAAATGATTGCATGTGAACGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTCTTGTAAAGGTGCAGATGAGGATAAAACCAAATGATTGCATGTGAACGTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 126

TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttc ... ttactgtcagGTTTCTTCAGAAGAATCAGATCACCTTCTTTACCTCTGCGTACGATGGTTCTTGTAAAGGTGCAGATGAGGATAAAACCAAATGATTGCATGTGAACGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAATTGCCAGAGCTACTTGCTTCTGTCAATATGGAGGAAGATGCGTTGAACAAGCTACAGCTGAAACTGCTGGACGTTCTCAAgtatgctttcttgcttcagagttatgcttgcaacctttttagcttaacctgaatcattccaatggctttactgtcag

- - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA