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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgtgatactgcgtattttcataattcttcatcttactctctgattatgtttttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG

Basic information

species Zea mays
transcript GRMZM5G844195_T03
intron # 17
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 18
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 17
gtatgtttgtgatactgcgtat-----tttcataattcttcatcttactctctgattatgtttt-taatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
||||   ||| | | |   | |     || ||||| ||| ||| | |   | | | ||  |||  || |  |||| |||||||| |||||| ||||||| |||||||||||||||||||||||||| ||||| |||||||||||||||||  ||
gtattgctgtaacaattgatttatgctttccataactctgcatatca---tgtaactacctttcatattacagGCGGCCAATGATTGTGATCTGGAACCGGTTGCTTATGAGTTCTTTACTCAAGCATTCATCTTATATGAAGAAGAAATTGCG

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 16
------------gtatgtttgtgatactg---cgtattttcataattcttcatcttactctctgattatgttttta-atttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
             | || || | | |       |   |||| ||| | ||        |   || || | || ||  ||| ||||||| ||||||||||| |||||||| ||||||||||| || || || ||||| |  ||| ||||||||||||||||  | 
gtactggaatatatttggttatcacatcaaaatgatatttcctaactatttgctgattttgttgtttcttttcttgcattaagGCTGCAAATGACTGTGAATTGGAACCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 16
--------gtatgtttg--tgatactgcgt-attttcataattcttcatcttactctctgattatgtttttaattt-----------agGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
         ||| ||||  || || ||| | |   | ||| ||| | |   || |  |||||| | || ||  |||           ||||||| ||||||||||| ||||| || ||||||||||| || || || ||||| |  ||| ||||||||||||||||  | 
gtacttgaatatatttggttgttagtgcatcaaaatgatatttcctaactatatttgctgattttattgtttctttttcttgcattaagGCTGCAAATGACTGTGAATTGGAGCCTGTTGCTTATGAATTTTTCACCCAAGCTTATATTCTATATGAAGAAGAAATTTCT

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 18
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 16
----------------------gtatgtttgtgat----actgcgtattttcataattcttcatcttactctctgattatgtttttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
                      || | |     ||    ||     |     ||| | | | | || |   | |  || | ||     ||||||| || ||| ||||||| || ||| ||||||||||||||||||| ||  | || |   || | ||||||||||||||  | 
gtatatgatcatttggactttggtgtatccactatcaaaaccaacaaaagatatagtgcatgagctgaaattttc-ttttattgaatctttagGCAGCAAATAACTGTGAGTTAGAAACAGTTGCTTATGAGTTCTTCACAAAGGCATATCTTCTGTATGAAGAAGAAATTTCA

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------------gtatgtttgtgat-----actgcgtattttcataattcttcatcttactctctgattatgtttttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
                                    |||| |||       | ||  | |||   |||  ||  || |||  |  |||| |  ||  |||   ||||||| |||||||||||| | || || ||||||||||| || || ||||| || ||||| || ||||||||||||||  ||
cactgaacagagtctttaatattgttactgactaggtgttggtgggcaagaattgtttgtttctctaac-ctgtat-ttataccttgatca--ttgataacc-agGCTGCTAATGACTGTGATCTTGAGCCTGTTGCTTATGAATTTTTCACTCAGGCATTCATATTGTATGAAGAAGAAATTGCG

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 18
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------------gtatgtt-tgtgatactgc-gtattttcataattcttcatcttactctctgattatgtttttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
                                 ||      ||| | |  ||  | ||  |   |  |  |||||| || | ||||| |||  |  ||  ||||||| ||||| |||||||||||||| ||||||||||| || || || ||||| | ||| || ||||||||||||||  ||
gtacatgagtatgttttgtgttaaaaatcattggtggaccatgtaacaaagctatgttagctctaaccagcatctt-ctttttgattttgtaat--atacagGCTGCAAATGATTGTGATTTGGAACCTGTTGCTTATGAATTTTTCACCCAAGCTTACATATTGTATGAAGAAGAAATTGCG

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|9952706|gb|BE639169.1|BE639169
EST:     GTGTTCCTTCCCCAGAGGTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|31355991|gb|CD440348.1|CD440348
EST:     GTGTTCCTTCCCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|31353910|gb|CD438267.1|CD438267
EST:     GTGTTCCTTCCCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|31355451|gb|CD439808.1|CD439808
EST:     GTGTTCCTTCCCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|78088719|gb|DV517112.1|DV517112
EST:     GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgcgtattttcataattcttcatcttactctctgattatgtttttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG
                                            ttttaat  putative branch site (score: 3)
                                         tgttttt  CT-rich tract
                                 tctgattatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgtgatactgcgtattttcataattcttcatcttactctctgattatgtttttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA