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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctcttgattctgttgtgaactaacgtggcaccatattatacttggtaaatgacaagtctaacttgatttttctctcatgtctgttgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC

Basic information

species Zea mays
transcript GRMZM2G005849_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005849_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 2
atcctcttgattctgttgtgaactaacgtggcaccatattatacttg-gtaaatgacaagtctaacttgatttttctctcatgtctgttgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC
| |||| |||| |  |    || ||| || |||  | || ||| |   |||||     |   |  | | ||   |   | || |||| ||  |||| ||||||  |||||||||||||||   ||||||| |||||||||||||||||||| ||||||||||||||||||||| | |||||||| |||||||||||  | |
aacctcatgataccatctcaaattaatgtagcaagagatgataatgatgtaaacagataaatttccatcataacttggt-atttctgatgtatctgctcagGTTCTGAAAGAGACACTAATCCGGCACGGGTTCACCTTTGAGTCTGATACTGACACAGAAGTCATCCCTAAGTTGGCAAAGTTTGTTTTTGATAAGGCGC

upper sequence: GRMZM2G005849_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 2
atcctcttgattctgttgtgaactaacgtggcaccatattatacttg-gtaaatgacaagtctaacttgatttttctctcatgtctgttgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC
| |||| |||| |  |    || ||| || ||| || || ||| |   |||||     |   |  | | ||   |   | || | || ||  |||| ||||||  |||||||||||||||   | || || |||||||||||||||||||| ||||||||||||||||||||| | |||||||| |||||||||||  | |
aacctcatgataccttctcaaattaatgtagcaacagatgataatgatgtaaacagataaattcccatcataacttggt-atttttgatgtatctgctcagGTTCTGAAAGAGACACTAATCCGACATGGGTTCACCTTTGAGTCTGATACTGACACAGAAGTCATCCCTAAGTTGGCAAAGTTTGTTTTTGATAAGGCAC

upper sequence: GRMZM2G005849_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 2
atcctcttgattctgttgtgaactaacgtggcaccatattatacttggtaaatgacaagtctaacttgatttttctctcatgtctgt-tgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC
        |   || |     ||  ||           |  |  |   |   | |    ||| | |   | ||||||  ||||   | ||  | ||||||||| ||||| ||||| ||   ||| || |||||||||||||| ||||| || ||||| || |||||||| ||||| || ||||| ||    || ||  |  
----gtaaggcgctctctcatacacactccatgtggc-tagtgttgcatgttttatctctctga-tcagtgtttctcagatgttattgtgtgtgtgttcagGTTTTGAAGGAGACGCTGCTTAGACATGGCTTCACCTTTGAATCTGAAACTGACACCGAGGTCATCCCCAAGCTTGCCAAGTTTGTCCACGACAAGGCGA

upper sequence: GRMZM2G005849_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 2
----------atcctcttgattctgttgtgaac---taacg-tggcaccatattatacttggtaaatgacaagtctaact---tgatttttctctcatgtctgttgat-tctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC
           ||   |  | |||    | |||   ||| | || |||  | || |   | ||     ||   | || ||   || |  || | ||     | ||  | | ||||||||| ||||| || || ||     | || |||||||||||||| ||||| || ||||| || ||||| || ||||| |||||||| |||| ||| ||  |  
gtaacgttctctctcatacactctaaattaaacgcctaatgatgccactctgttgtggctagtgctgtacgt-tttatctctctgttcgttgtttctcagatattattgtgtgttcagGTTTTGAAGGAAACGCTGCTCCGACATGGCTTCACCTTTGAATCTGAAACTGACACTGAGGTCATTCCCAAGCTTGCAAAGTTTGTTTATGACAAGGCGA

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|211507108|gb|FK960922.1|FK960922
EST:     CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAG                         GTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
genomic: CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAGgtctgcttac ... ttctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
EST: gi|89758439|gb|DY687617.1|DY687617
EST:     CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAG                         GTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
genomic: CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAGgtctgcttac ... ttctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
EST: gi|149014772|gb|EE044464.2|EE044464
EST:     CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAG                         GTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
genomic: CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAGgtctgcttac ... ttctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
EST: gi|149081060|gb|EE170160.2|EE170160
EST:     CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAG                         GTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
genomic: CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAGgtctgcttac ... ttctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACA
EST: gi|149005284|gb|EE039833.2|EE039833
EST:     CCGGTGATGAGTTCTTGGTTGTTCACAATGGCATTATCACCAACTATGAG                         GTCTTGAAAGAGACACTAACTAGG
genomic: CCGGTGATGAGTTCTTGGTTGTCCACAATGGCATTATCACCAACTATGAGgtctgcttac ... ttctgttcagGTCTTGAAAGAGACACTAACTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaaatgacaagtctaacttgatttttctctcatgtctgttgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC
                                             ttctgttc  CT-rich tract
                    ttgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctcttgattctgttgtgaactaacgtggcaccatattatacttggtaaatgacaagtctaacttgatttttctctcatgtctgttgattctgttcagGTCTTGAAAGAGACACTAACTAGGCACGGCTTCACCTTTGAGTCTGATACAGACACAGAAGTCATCCCTAAGCTAGCAAAGTTCGTTTTTGATAAATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - ctgttgt
- - - - - - - - - -gaactaa
- - - - - - - - - - - - - - -ggcacca