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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcctatatctgatagaatcagcactgtaaacacacagtctgccatataatctatttgaggtctcaaacgttcatccatgtttcttgctctttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG

Basic information

species Zea mays
transcript GRMZM2G039263_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 9
----ttcctat-atctgatagaatcagcactgtaaacacacagtctgccat-ataatctatttgaggtctcaaacgttcatccatgtttcttgctctttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG
    || ||||  | |  | ||||  |   || |  ||||||   | | || ||||| |||    |||||| ||   | |  |||  | ||| || ||  |  |||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||  ||||||| ||||||||||| ||||||||  |||||
tttatttctattgttttgtggaatgtg-gttggatccacacataattctattataatttat----ggtctccaattgtaaaacataat-cttacttttcatggcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTACTGACCACTAAGGGAATTGATGATATGTCACTGAAG

upper sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
ttcctatatctgatagaatcagcactgtaaacacacagtctg--ccatataatctatttgaggtctcaa-acgttcatccatgtttcttgctctttttct--cagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG
        | |  ||  ||   ||    ||       ||||    | | ||||   |||| ||  |      | |    ||       | ||  | |  |  ||||||| |||| || || || ||||||||||||||| |||| || |||||||| ||||||||  | || || || || ||||| || ||| |  | |||
-----gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagcactaactgtacttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG

upper sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
ttcctatatctgatagaatcagcactgtaaacacacagtctgccatataatctatttgaggtctcaaacgttcatc--catgtttcttgctctt-----tttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG
    ||||| ||      |   ||| |   |         |  ||| |  | ||||        |||   ||  ||  | | ||  |      |     |||  ||| ||| | ||||| || || |||||||||||||||||||||||||| || ||||||||  |  | || || ||||| ||||| |||||||| || |||
----tatat-tggggagtttgtcacgg--gatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG

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|31406088|gb|CD484820.1|CD484820
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|211239408|gb|FL328610.1|FL328610
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|33104341|gb|CF064301.1|CF064301
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|211157236|gb|FL334269.1|FL334269
EST:     AAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: AAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|211149768|gb|FL359580.1|FL359580
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|7238110|gb|AW573332.1|AW573332
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|211195400|gb|FL324707.1|FL324707
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|60343155|gb|DN210128.1|DN210128
EST:     GTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|33102590|gb|CF062550.1|CF062550
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|31440979|gb|CD510410.1|CD510410
EST:     GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     GTCCAAGTTCTTGTAGCTGATCCAAGGGAACTTGAGAAGATTCGTCAGAG                         AGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC
genomic: GTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGC

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: 675

GAATTGCTTGTCTTGATTTTAACCTTCAGAAGACAAAAATGCAACTTGGTGTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 306

GAATTGCTTGTCTTGATTTTAACCTTCAGAAGACAAAAATGCAACTTGGTGTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

GAATTGCTTGTCTTGATTTTAACCTTCAGAAGACAAAAATGCAACTTGGTGTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 258

GAATTGCTTGTCTTGATTTTAACCTTCAGAAGACAAAAATGCAACTTGGTGTCCAAGTTCTTGTAACTGATCCAAGGGAACTTGAGAAGATTCGTCAGAGgtatttgcat ... tttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataatctatttgaggtctcaaacgttcatccatgtttcttgctctttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG
                         ttcatccatgtttctt  CT-rich tract
     tctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcctatatctgatagaatcagcactgtaaacacacagtctgccatataatctatttgaggtctcaaacgttcatccatgtttcttgctctttttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG