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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcaccaagtcttggtttgaaactttgtagcatctgagatggaaaatctcatagtgatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT

Basic information

species Zea mays
transcript GRMZM2G331032_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 12
gtatgtgcaccaagtcttggt-ttgaaactttgtagcatctg------agatggaaaatctcatagtgatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT--
||| |||||   | |  |  | | ||| |||| || ||  |       || |   || ||   | | ||| ||| |||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||| |  ||   | | |||    
gtacgtgcagggaatgctaatatagaacctttttaacacataccagacagttcagaactcatgttgagatgcatattccagGTGTGGGAGAAGAGCGGTTACAACACCGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCGATGAAG--AAAAAAGTCCC

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------gtatgtgcaccaagtcttggtttgaaactttgtagcat-ctgagatggaaaatctcatagt--gatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTT-AGCAACAAATCCATACAAGAT
                           || ||   |  |||||  |   ||| |   |   || ||    |     | || |   |  |  ||  ||  ||||||||||||||||| ||||| ||||| || ||||||||||| ||||| || |  || ||||| || ||||| || || | | ||  |||  ||    ||  
tcttttatgtgatttgcgttttggttaatctgtctctggtctt--tcaaaaattgattgctatactacttttttggacctgactatccggaacgattggcagGTTTGGGAGAAGAGCGGTTACAACACGGTCGAGTGGGTTCGATACATAACGAAAGCGGGATCTTACGAGATCAGATGCTGAACATTAAACACAGTTCAGG-

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------------gtatgtgcaccaagtcttggtttgaaactttgta-gcatctgagatggaaaatctca---tagtgatac---attt-tccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGC--AACAAATCCATACAAGAT
                      |   ||  | |||| ||   | | |  | |  |  |     | | ||||   ||||   | ||||||    |||| || |||| |||||||| |||||||| | ||||||||| ||||| |||||||||||||| || || ||||| || ||  |||| ||       | ||     || |  
gtccgttctctacccctgcctctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACAAGAGCCGGTTCATACGAAATTCGGTGCTAATTTGGAACATTTGCCCATG--

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S197_28V6.1 (Physcomitrella patens), 3'ss of exon 11
-----------------------------gtatgt--gcaccaagtcttggtttgaaactttg---tagcatctgagatggaaaatctcatagtgatacattt-tccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT
                             | |||   ||  |||   |     || |   | |   | |||  | |  |    |   || |||      || | | ||||| ||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| || || ||||| ||  |||| |                     
gtgggttccttctccgtatgtgtaatatcgcatgatagcttcaatggtgcacatgcagactggattttgcaagtaactttctcatgttcgtagctgcttatctgttcagGTATGGGAGAAGAGTGGTTACAACACTGTTGAATGGGTGCGCTACATCACAAGGGCCGGTTCTTATGAAATCCGGTGCTGA-------------------

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 12
gtatgtgcaccaagtcttggtttgaaactttgtagcatctgagatggaaaatctcatagtgatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT
      | |   |  || |    ||   |||      ||||  |||    || || |  ||      |   ||||| ||||| |||||||| || | ||| || || ||||| |||||||||||||| |||||||| || || |||||||| ||  || |  |      | |  
------gtaagcaaactcgtcgcgattgtttaggaattctggaatg----atttctttctg----gctcctcagGTGTGGGAAAAGAGTGGATACAGCACAGTGGAATGGGTACGCTACATCACAAGAGCTGGATCGTACGAAATAAGGTGCTAAAAAAACGTGAGGGAAGGGA

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|149083895|gb|EE173270.2|EE173270
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|60356037|gb|DN223010.1|DN223010
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|5847424|gb|AW000503.1|AW000503
EST:     GTTCCAATGTTCNCTGCNTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|4886096|gb|AI677216.1|AI677216
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCCCA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|78022244|gb|DV490631.1|DV490631
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|60354626|gb|DN221599.1|DN221599
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|6012529|gb|AW061966.1|AW061966
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAAAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCCCA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|7145566|gb|AW507047.1|AW507047
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTG-T-ATAACACTGTTGAGTGGGTT
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTT
EST: gi|37396642|gb|CF635614.1|CF635614
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|76282278|gb|DV021846.1|DV021846
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|71304028|gb|DR788135.1|DR788135
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|211534676|gb|FL445694.1|FL445694
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|211271326|gb|FL168764.1|FL168764
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAASAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|6101968|gb|AW126438.1|AW126438
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|37375113|gb|CF623970.1|CF623970
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|4609486|gb|AI600325.1|AI600325
EST:     GTTCCAATGTTCNCTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|91054997|gb|EB165415.1|EB165415
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|31250241|gb|CD219265.1|CD219265
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|32932355|gb|CF037167.1|CF037167
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|32932405|gb|CF037217.1|CF037217
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
EST: gi|37383436|gb|CF628735.1|CF628735
EST:     GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAG                         GTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA
genomic: GTTCCAATGTTCACTGCTTCTGGTTTACGTGTTCGCTTCCTTAAGgtatgtgcac ... cattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgaaactttgtagcatctgagatggaaaatctcatagtgatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT
                                             cattttcc  CT-rich tract
                                          atacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcaccaagtcttggtttgaaactttgtagcatctgagatggaaaatctcatagtgatacattttccagGTTTGGGAGAAGAGTGGTTATAACACTGTTGAGTGGGTTCGCTACATCACAAGGGCTGGATCATATGAGATAAGGTGTTAGCAACAAATCCATACAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA