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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaatttcttttgggtgtaaaacttcacaaatctgcatgctatcttatgtttcagcaccattctactgcgactgttgtgatatt...

Basic information

species Zea mays
transcript GRMZM2G133029_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g56930.2 (Oryza sativa), 5'ss of exon 4
TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaatttcttttgggtgtaaaacttcacaaatctgcatgctatcttatgtttcagcaccattctactg-cgactgttgtgatatt----
|||||||||||||||||||||| |||||||||||||| ||||| || |||||||||||||| |||||||||||||| ||||||||||| || |||||||||| ||| |||| |  | ||||| ||| |   |||| ||||||| || |||||    | | |  |  |  |  |   ||| ||     | |||    | |||    
TCTCTCATTGCCTGAAAGGTTCAGATAATGGTGGTGGTATTCTCGTTCTTGGTGAAATTGTCGAGCCAGGATTAGTCTATACTCCACTCGTCCCATCACAgtgagtctcttac--tagaattacttat---tgtataacttcagaattctgctgattttttgtttgtagaaaagttttcaaccaataagtgtatgcacattcatt

upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA11G19640.2 (Glycine max), 5'ss of exon 4
TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaatttcttttgggtgtaaaacttcacaaatctgcatgctatcttatgtttcagcaccattctactgcgactgttgtgatatt---
|||| ||||||||||||||     ||| |||||||||  |  | || |||||||||||||||||||||    |||| |||| ||||||||||||||||||||| |||  |||  || || | | |  |  || | ||  |    | |||    |  |   || || ||  |     | ||| |     || |||    |    
TCTCCCATTGCCTGAAAGGAGATAATAGTGGTGGTGGTGTATTGGTTCTTGGTGAAATTGTGGAGCCAAACATAGTTTATAGTCCACTTGTTCCATCACAgtacgttcatttg-ttagagtatatgctacgtttcaatttctttatatcaat-tatttatttgtggttttgttgtgtgcta-tatacatgctgtttcctcggc

upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G05490.1 (Glycine max), 5'ss of exon 4
TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaat-----ttcttttgggtgtaaaacttcacaaatc-tgcatgctatcttatgtttcagcaccattctactgcgactgttgtgatatt
|||| ||||| ||||||||      || |||||| |||||  | || |||||||| ||||||||||||    |||| || ||| ||||||||||| ||||||||||| ||||| |  ||||      | |  |   | ||    ||   ||||  |  |||||   |   | |  | |   | |    ||  |  || ||||    
TCTCACATTGTCTGAAAGGAGATAGTAGTGGTGGGGGCATATTGGTTCTTGGTGAGATTGTGGAGCCAAACATAGTCTACACTTCACTTGTTCCAGCACAgtaagttcctttcatcagaataaaacctatgctttttttagtgtttgctaaataataaatgcttgatgggggt--aacttgaattatttggtaaagtagtga----

upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G07270.1 (Glycine max), 5'ss of exon 4
TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaatttcttttgggtgtaaaacttcacaaatctgcatgctatct----tatgtttcagcaccattctactgcgactgttgtgatatt
||||||||||| | || ||    |  ||||| || |||||||| || |||||||| ||| |||||||| |  | || |||| ||||||||| ||||||||||| |||   ||| |      || | |    |      |      | |    |   |  |     ||| ||| | ||   || ||    || |||         
TCTCTCATTGCTTAAAGGGAGACGGCAATGGAGGAGGCATTCTAGTTCTTGGTGAGATTTTGGAGCCAAGTATTGTTTATAGTCCACTTGTCCCATCACAgtatgttctcttcttcacttcttttctcattttctttccccagttagttgataatttccccctaatattttttaacattgttgtaaaaggaatgtacaag----

upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA12G08870.1 (Glycine max), 5'ss of exon 4
TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaatttcttttgggtgtaaaacttcacaaatctgcatgctatcttatgtttcagcac-cattctactgcgactgttgtgatatt--
|||| ||||||||||||||     ||| |||||| ||| |  | || |||||||||||||||||||||    |||| |||| ||||||||||| ||||||||| |||  |||  | |     | |  |   | | ||  |    | |||       ||| |   ||||   ||     | ||      ||| |       |  
TCTCCCATTGCCTGAAAGGAGATAATAGTGGTGGGGGCGTATTGGTTCTTGGTGAAATTGTGGAGCCAAACATAGTTTATAGTCCACTTGTTCAATCACAgtacgttcatttgttagag---tatgctacatttcaatttctttatatcgattatttatttgtggttttctcatgtgctatatacatgctgctcatcggctga

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|32928121|gb|CF032933.1|CF032933
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|14203670|gb|BG837347.1|BG837347
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCAYTTGTTCCATCACA                         GCCTCATTACAAYTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|84976772|gb|DW475194.1|DW475194
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|211449625|gb|FL035069.1|FL035069
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|74234970|gb|DT642884.1|DT642884
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|149044646|gb|EE047618.2|EE047618
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTTCATCACA                         GCCTCATTACAACTTAAATCTGGGAAAGCATTGCTGTC
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGG-AAAGCATTGCTGTC
EST: gi|60339993|gb|DN206966.1|DN206966
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|32931524|gb|CF036336.1|CF036336
EST:     GTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|211449626|gb|FL035070.1|FL035070
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
EST: gi|148961307|gb|EE012032.2|EE012032
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACC                         GCCCTCATTACACCTTAAATCTGGAAAGCATTGCTGTCA
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCC-TCATTACAACTTAAATCTGGAAAGCATTGCTGTCA
EST: gi|149108251|gb|EE292593.2|EE292593
EST:     GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACA                         GCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT
genomic: GGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttct ... tgaaatatagGCCTCATTACAACTTAAATCTGGAAAGCATTGCTGTCAATGGTCAAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTCATTGCCTGAAAGGTTCGGATAATGGTGGTGGCATTCTTGTGCTTGGTGAAATTGTGGAGCCAGGATTAGTGTATACTCCACTTGTTCCATCACAgtaagtttctttccttggaatttcttttgggtgtaaaacttcacaaatctgcatgctatcttatgtttcagcaccattctactgcgactgttgtgatatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG