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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatcatacactttgttagaaaggtgaaattttacttgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtacaaacacatttcaattccattttcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG

Basic information

species Zea mays
transcript GRMZM5G844195_T03
intron # 13
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 14
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 13
gtgagatcatacactttgttagaaaggtg-aaattttacttgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtacaaacacatttcaattccattttcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG
                     | ||  |  |   || | |      || |||| |   || |   | |||    |  |  |||||| ||  |||||  || |||   |||            ||||||| || ||||||     || ||| | | || |             ||||||||||| || || |||||||||||||| || ||||| |||||||| ||||||||| ||||||||||||| | |||||||||| |||||
---------------------gtaatatacacgcttcattctacaattttctttggcttgttatattgtttctgc--tgctgttcaactgaatcagcgcacacaatattc-----------tattttcttatcaagttt-----acctgttatattgct-------------tagCTTGATGATGAGGATTTTAAGGAGGAACAGAATTCTGTGGCGCGTCTTATTCACATGTTGCACAATGATGACCATGAAGAGATGTTGAAG

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 14
-----------------gtgagatcatac-actttgttagaaaggtgaaattttacttgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtacaa-acacatttcaattccattttc-attttctcatgaagtttgctcaacttgtaac-------aatgttcttttaattatttta--gCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG
                  |   ||| |   | ||||||   ||||  | | ||    | | ||   | ||  || |  |  ||  |     ||| |||  |    ||  |||   ||| | | | |  | |   |||  | |  |    || |  |||||||||  |   ||       ||| || ||  |  |  |  |  | ||||||||||||| || || ||||| ||||| ||||| || || ||||| |||||||| || |||||||| || || || ||| | || 
ggtgtgcctgagttttgttattatcttgggattttgtttataaggatacaattgttctatgtgacctgttattttt--taattgatatattcaacatttcttta-tatgtcaaagcaataaataatctattattattccctacataaatataatatttgctcaagatcagaccaatttaaatatttttccatcttgtacacaGGTTGATGAAGAAGATTTCAATGAGGAGCAAAATTCTGTCGCTCGCCTCATACACATGCTTCATAATGATGAACCAGAGGAAATGTTTAA-

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 13
--------------gtgagatcatac-actttgtt-agaaaggtgaaattttact-tgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtaca-aacacatttcaattccatt------ttcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG
               |   ||| |   | |||||| | |||| |   ||| | || |||    |||  |  ||    |  ||| ||  |      || |   |  | | || || | ||   |||   ||||| |       |  | | | |  | ||| |    | | ||  || | | |||  |    ||    || ||||||||||||| || || ||||| ||||||||||| || || ||||| |||||| | || ||||||||  | || || ||| | |||
gtgtgcctgagtatttattatcttgggattttgtttataaagatatgattgttctctgtgacctgttatttttgaattatttatttaacatttctttatat-gtcaaagcaataaataatctattattattccctacataaatataatattttctcaagatcatcctattttaaatatttttccatcttatacac-agGTTGATGAAGAAGATTTCAATGAGGAGCAAAACTCTGTTGCTCGCCTCATACACATGTTTCATAATGATGAATCAGAGGAAATGTTTAAG

upper sequence: GRMZM5G844195_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 13
gtgagatcatacactttgttagaaaggtgaaattttacttgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtacaaacacatttcaattccattttcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG
                                      || | | || | ||  | ||  | |||  ||||   | |||   |    |||||  ||| | | |     ||||     |||  ||||||      |||| ||  |  || ||||||                 |||||||||| || || || ||||| |||||||| ||||| || |||||||| |||||| |  |||||||||| || ||||| ||| |||||
--------------------------------------ttttattttattttt-tccttttactttcttcttgaattatcactg---tagattggtatagataa----caatc----tttgtttttctt-----gtttacttta--tgcaacaat-----------------agCTTGATGAGGAGGATTTCAAGGATGAACAAAATTCTGTCGCTCGTCTCATACACATGTTCTACAATGATGACCCCGAAGAAATGTTGAAG

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|31355991|gb|CD440348.1|CD440348
EST:     ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAG                         CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcat ... attattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
EST: gi|31353910|gb|CD438267.1|CD438267
EST:     ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAG                         CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcat ... attattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
EST: gi|31355451|gb|CD439808.1|CD439808
EST:     ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAG                         CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcat ... attattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
EST: gi|33094690|gb|CF054684.1|CF054684
EST:     ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAG                         CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcat ... attattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
EST: gi|33094433|gb|CF054427.1|CF054427
EST:     ATTTAATTAAGGGGCTGATAAAGGATATGGGTGGAGCTCAAGATGATGAG                         CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcat ... attattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
EST: gi|78088719|gb|DV517112.1|DV517112
EST:     ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAG                         CTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT
genomic: ATTTAATTAAGGGGCTGATAAAGGATATGGATGGAGCTCAAGATGATGAGgtgagatcat ... attattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG
                                              ttatttt  CT-rich tract
                          ttgtaacaatgttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatcatacactttgttagaaaggtgaaattttacttgtttgttgtcttcgttctgatgcttagttctcccaatattgttcagctagatcagtacaaacacatttcaattccattttcattttctcatgaagtttgctcaacttgtaacaatgttcttttaattattttagCTTGATGAAGAAGACTTTAAGGAGGAACAAAACTCTGTAGCGCGTCTCATTCACATGCTGCACAATGATGATCCTGAAGAGATGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG