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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatttttctctatgtacttcaaaattcaaattccaacttaaacttagctcccagcgaaaagaagaaaacatctagcatgatatagtaactcgaagctgatgcattgtatactgttaaagctgagtttgaagtgttgtgcattttgtttgtttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTCATTGTAGCAGTACTCCTTGACAACACACTTGATGTGAGAGATGCAGCAA

Basic information

species Zea mays
transcript GRMZM2G100484_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100484_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os09g15170.1 (Oryza sativa), 3'ss of exon 13
gttcgtatttttctctatgtacttcaaaattcaaattccaacttaaacttagctcccagcgaaaagaagaaaacatctagcatgatatagtaactcgaagctgatgcattgtatactgttaaagctgagtttgaagtgttgtgcattttgtttgtttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTCATTGTAGCAGTACTCCTTGACAACACACTTGATGTGAGAGATGCAGCAA
                                                       |||  |     |    || || |  |||  |   | || ||        | ||||||| |   ||| |   ||      | | |      |  || |  | ||| |||||||||||||||||||||||    |||||| || |||||  | |||||||||||  | || || ||||||||||||||||| ||||| ||||| || ||||
------------------------------------------------------tccattgttcttag---aatatttgacattttcctgcaagtctg------ttcattgtacatgtttacactggaaaccagaatttgaattgtgctgctcttgtgt-gcagTTCAATGACTACATCAACAGCGTCTTCTCGTCTCCACCGACTGTCGCCCTCATCATGGCGGTTCTCCTTGACAACACACTCGATGTCAGAGAGGCGGCAA
















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|71770760|gb|DR968697.1|DR968697
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|50334184|gb|CO529310.1|CO529310
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCATACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|166541115|gb|EG070021.1|EG070021
EST:     GGTATTCGACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCT
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCT
EST: gi|9461889|gb|BE453955.1|BE453955
EST:     GGTATTCCACAAGTTCTCACCAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|78086984|gb|DV515377.1|DV515377
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTTTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|89763225|gb|DY690516.1|DY690516
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|60398289|gb|DN231105.1|DN231105
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|50334185|gb|CO529311.1|CO529311
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCATACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|211271038|gb|FL034395.1|FL034395
EST:     GGTATTCGACAAGTTCTCAACAAGGCCCAGCACACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACC
EST: gi|21626173|gb|BQ621094.1|BQ621094
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|9566277|gb|BE475786.1|BE475786
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
EST: gi|71430812|gb|DR811862.1|DR811862
EST:     GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGG                         TTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC
genomic: GGTATTCCACAAGTTCTCAACAAGGCCCAGCGCACACAAAAGCTGGATGGgttcgtattt ... tttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatactgttaaagctgagtttgaagtgttgtgcattttgtttgtttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTCATTGTAGCAGTACTCCTTGACAACACACTTGATGTGAGAGATGCAGCAA
                                         tttgttt  CT-rich tract
                                   attttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtatttttctctatgtacttcaaaattcaaattccaacttaaacttagctcccagcgaaaagaagaaaacatctagcatgatatagtaactcgaagctgatgcattgtatactgttaaagctgagtttgaagtgttgtgcattttgtttgtttgttgcagTTCAATGACTACATCAACACTAGCTTCTCATCACCACCCGCCGTCGCCCTCATTGTAGCAGTACTCCTTGACAACACACTTGATGTGAGAGATGCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG