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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA

Basic information

species Zea mays
transcript GRMZM5G844195_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 11
gtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcat--tatatttgct--tggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA
                                                                       | | ||  | | | |||     | ||| |  |  |   |  || | |     ||  |  | |    ||||    || || |||||  ||  |||  |  ||||||||||||||| || |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| |||||||
-----------------------------------------------------------------------agtcttcatggag-tatgcgccacagccactcccttg-gtgatgcctcttatgtcatgtatt----attgcgctttttagctcatgttaagtttaatgttggacagGGTGCATGCGTAAAGAAACTTTCAGGGAATGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTCAGTGCCCCCCTGGAGAAATATA

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 12
gtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA
                                                                             | |  | || | |   ||  ||      | |||  ||    ||  |  |  | | ||    ||   |   ||   || ||        |||  |||||| ||||||||||||| ||||| || ||  |||| ||||| || |  || |||||||||||| ||||||||||| | |||||||| || || |||||  
---------------------------------------------------------------------------ggtatgttactttcaaacatcacagcctctttatgagatgtggtatggacaaga-attgcattttagcttagctgcatcgtttctggaatttgtgcaGGGTTCATGTGTCAAGAAGCTTTCTGGAAAACCAAAGCTTGATGACAATAGAGCAACAAAGCAAGTTGTTGCACTTTTAAGTGCTCCACTTGATAAATAC-

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA
                                                                  |||    | ||  |    | |||   | |    |   ||      | |    | |  | ||| |||||      ||||       ||  |  | ||| |||   ||||| |||||||| | |||||| ||  |    | |||||||||||||||||   ||||||| || ||||||||||| || ||||||||  |||| |||||||
------------------------------------------------------------------aagtt-ctgttcataaaaccataggagttgtttaataaacttcatatttttatggatgaagttcaatgctg---gaataactggtcttctccttttttctt---cagGGAGCATGTGTTACGAAACTCTCTAGTGCTGGAAAACTTGAAGATAGCAAATCAACAAAACAGATTGTTGCACTACTAAGTGCTCCATTGGAGAAATATA

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 11
gtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattg-atagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA
                                                                         ||| ||| |   |   |  | ||      |||    |  | | ||| | ||  ||| |||||         | ||||  ||  | ||| ||  ||  |||||| |||||||| |||||||| || |||||| |||| ||||||||||| | ||||||||| ||||||||||||||| | || || ||  |||| || || |
---------------------------------------------------------------------ttcctttgtgtggaattcagagagcatctttgtgcagct-tagattgcataaatga-agttcaatgatggg-aggttttcttccttttgataatt--tttcacagGGAGCATGTGTTAAGAAACTCTCTGGCAAGCCAAAGCTTGAAGATAGTAAGGCAACAAAACAAATTGTTGCACTTTTGAGCGCCCCATTGGAGAAGTACA

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|19058370|gb|BM737037.1|BM737037
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|18963630|gb|BM660543.1|BM660543
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|33094690|gb|CF054684.1|CF054684
EST:     GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|87153186|gb|DY397975.1|DY397975
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAGGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|33094433|gb|CF054427.1|CF054427
EST:     GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: GTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|19058197|gb|BM736864.1|BM736864
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|18963632|gb|BM660544.1|BM660544
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
EST: gi|19057727|gb|BM736394.1|BM736394
EST:     TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTG                         GGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG
genomic: TTACTCTCCGTGTACATCCTGATCGGCTTGATTATGTTGACCAAGTGCTGgtaagtcttc ... gcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA
                           ttctaac  putative branch site (score: 1)
                                          tttgctt  putative PPT
                              taactcattatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttctttaaacaactatatgatgtatgccccttctcttatggtctgtttgctgactcagcaagccattttttgttgtgctataattgatagcaaggcaatgatgcaatccattagtggtagtacaatgtcaattgaatcttctaactcattatatttgcttggacagGGTGCATGTGTCAAGAAACTTTCAGGCAAGGCAAAACTTGAAGATAGCAGGGCAACAAAGCAAATTGTTGCACTTCTTAGTGCTCCCCTGGAAAAATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA