Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagaactttttatgcactaattaagaagaagtttgtgcaaattaagagctgcgcgcatgcatgggtctcgagactgaaatcacatatataatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG

Basic information

species Zea mays
transcript GRMZM2G075333_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075333_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 3'ss of exon 5
taagaactttttatgcactaattaagaagaagtttgtgcaaattaagagctgcgcgcatgcatgggtctcgagactgaaatcacatatataatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG
              | |||||| |     || |    ||||   |||   |  |    |  ||    ||  | | |    | |||  | |   ||  |||||||| |||||||||| |||| ||||||| ||||||||||| ||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||
--------------gtactaatcacatgcaaatgacagcaa--caaggattctg-atttaaatcttgct-aaaatttttctgacacgttt---gcaacagGTGGTGTTCTACAAGAGGATCAACAAGGTGTTCTTCACCGATTCCATCCCCAAGAACCCTTCCGGCAAGATCCTCAGGAAGGACTTGAGAGCCAGGCTCG
















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|37385300|gb|CF629786.1|CF629786
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|33098523|gb|CF058483.1|CF058483
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|91872376|gb|EB402333.1|EB402333
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTTTACAAGAAGATCCACAAGGTCTTTTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|37378779|gb|CF626098.1|CF626098
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|5740686|gb|AI948376.1|AI948376
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|7304669|gb|AW600608.1|AW600608
EST:     AATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|14208215|gb|BG841893.1|BG841893
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|149084820|gb|EE174324.2|EE174324
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|78021777|gb|DV490164.1|DV490164
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|45568048|gb|CK985876.1|CK985876
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|91053777|gb|EB164195.1|EB164195
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTTTACAAGAAGATCCACAAGGTCTTTTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|14243060|gb|BG840786.2|BG840786
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|32917036|gb|CF021848.1|CF021848
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|149109199|gb|EE293185.2|EE293185
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTTTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|37384112|gb|CF629103.1|CF629103
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|71450117|gb|DR831167.1|DR831167
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTTTACAAGAAGATCCACAAGGTCTTTTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|37385990|gb|CF630164.1|CF630164
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|94474315|gb|EB703273.1|EB703273
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|113701577|gb|EE679081.1|EE679081
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|24934544|gb|CA452762.1|CA452762
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|148949766|gb|EC895249.2|EC895249
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|148970850|gb|EE021626.2|EE021626
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTTTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|71774578|gb|DR972456.1|DR972456
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|86473141|gb|DY239511.1|DY239511
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|74242637|gb|DT650551.1|DT650551
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|76287908|gb|DV027476.1|DV027476
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|8577311|gb|BE129948.1|BE129948
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|78109184|gb|DV527601.1|DV527601
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
EST: gi|18660517|gb|BM500903.1|BM500903
EST:     AAG-TTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCC
EST: gi|148953986|gb|EC899377.2|EC899377
EST:     AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAG                         GTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC
genomic: AAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCC

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: 42 (upstream exon), 49 (downstream exon)
Score: 13

GAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

GAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

GAACGATGACCTTGCTGGTGAAATCCCGGTCGCCTTCATCGTGCGGACCGAAGGTTCTCAAGTCACCGAGGATGAGATCAAGCAATTCGTCGCCAAGGAGgtaaaagcaa ... aatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagctgcgcgcatgcatgggtctcgagactgaaatcacatatataatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG
                                aaatcacatatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagaactttttatgcactaattaagaagaagtttgtgcaaattaagagctgcgcgcatgcatgggtctcgagactgaaatcacatatataatgctgcagGTGGTTTTCTACAAGAAGATCCACAAGGTCTTCTTCACCGAATCCATCCCCAAGAACCCGTCGGGCAAGATCCTGAGGAAGGACTTGAGAGCCAGGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - -tatgcac
- - - - - - - - - - - -aagaagaa
- - - - - - - - - - - - - - - - - - - - - - - gagctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaca