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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 19
--------------caattttct--tacatctcacagg---tagttaggaatctacaactaaaca-agcagacccttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT
              | | |||||    ||| ||   ||   |  |  | | | |  |    ||   ||  || ||||  | |||||     | |||| | |   ||||| | ||  ||||||||| ||||||||||| ||||||||||| || || || ||||||||||| ||||||||||||||||||||| ||||||| ||    ||||| ||||| |
gtatctctcactttccactttctacctcatttctttggatcttctctgcattttgtactacaatgcagaggatccttcttcattctatcaaccaattctttcacattatctgtgtcgcagCTCATTTGGGACCGTGCTCTTGGCCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAGAACCACTGCAAGAAGGTTGCTGCTTGAAGCT

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 19
caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattt-tgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT
         || || ||     |  | |    |||||  ||       |||| | |   | |  |   |  || | || || |  ||||| |||||  |||||||| ||||||||||| ||||| ||||| || || || ||||||||||| ||||||||||||||||| ||| ||||||| ||    ||||| ||||| |
--------gtatatttcttccct--tcaactgtctacctctttctt--cagatcttgtatcaaccaatt--ctgacttgtgatacattatgtatga--cagCTCATTTGGGACCGTGCTCTTGGTCTGCCGCTCGAAAGACCGAAGAGTGTCACCATGGAGTGGCTGGAAAACCACTGCAAGAAGGCTGCTGCTTGAAGCT

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 19
-caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAA---GGCTGCCTGAAGAT
  ||  |   || || | |||  |           ||| ||  ||||   | | |   | | ||  ||||  | | | |  ||||  | ||||     ||||| || |||||||| || ||||| ||  ||||||||||||| ||||||||||||||||| ||||| ||   | | || || ||        |||| | |    
gtaacatatatatat-ttacacattacgcctttgttactacataacatttaaaacagaactcata-tgctctccattctcatttg--tgtttaattcacagCTTATATGGGACCGAGCTCTTGGACTTGCACTTGAGAGGCCAAAGAGTGTTACCATGGACTGGCTTGAAGCCCATTGTAAGAAAGCTTCATCTGCTTAAG---

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 19
--------------------------caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattttgtttgattatttatgatg-cagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT
                             | ||||  | |  |  |  | ||| |   |||  ||     ||  |   |     ||   ||||      | | || ||  ||||||| |  |  ||| | || ||||||||||| |||||  |||| ||||||||||| || |||||||| ||||| ||||| || ||| ||||||| ||    || |||| |   |
gttctcactatgtccctcaccttcttttctcttctccctttccgtattttgtttgttttcttaaatctctcattcttccttcgggtgcatctg--aatcattattatt--attatttcttttctcagTTAATATGGGACCGTGCTCTTGGATTGCCCCTTGAGAGGCCAAAAAGTGTTACAATGGAATGGCTTGAAAACCACTGCAAGAAAGCAGCCGCCTAATTCT

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 20
lower sequence: EFJ25084 (Selaginella moellendorffii), 3'ss of exon 18
caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT
                                               | |    | | ||  |||      ||    |||  || ||   |||  | |||||  | ||||| || || ||||| || ||| |||| ||||| |||||  | ||||||||||||||||||||||| ||||| ||  |  | |    |   |
-----------------------------------------------gtactagcattgtgcttccaagctctccaattgactgcttg--tatccttcagCTGGTGTGGGATCGCGCACTTGGTCTTCCAATTGAAAGGCCAAAGAGCATGACCATGGAGTGGCTGGAGAACTATTGCAAGAAGCAAACCGTGACAGCGT

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|211314254|gb|FK994154.1|FK994154
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|6020672|gb|AW065480.1|AW065480
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGNGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGGT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|5847106|gb|AW000185.1|AW000185
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|67022591|gb|CO451340.1|CO451340
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|32859372|gb|CD999053.1|CD999053
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|4776524|gb|AI665527.1|AI665527
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|31361873|gb|CD446230.1|CD446230
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
EST: gi|149082724|gb|EE171942.2|EE171942
EST:     ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAG                         CTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT
genomic: ATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCAGgtctgccttg ... tatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcagacccttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT
                           taattttgtttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattttcttacatctcacaggtagttaggaatctacaactaaacaagcagacccttagtaattctgctggctaattttgtttgattatttatgatgcagCTCATCTGGGACCGTGCCCTTGGCCTGCCACTTGAGAGGCCGAAGAGTGTTACCATGGAGTGGCTGGAGAACTACTGCAATAACAAGGCTGCCTGAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA