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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattaccactgcacattgcatgatatcaatctgtcttcatccaatggagatccctgtattccatattgaagccattgtgattgatcatttttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG

Basic information

species Zea mays
transcript GRMZM2G147884_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 9
taattaccactgcacattgcatgatatcaatctgtcttcatccaatggagatc--cctgtattccatat-tgaagccattgtgattgatcatttttcgt-gcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG
     ||   |  ||| ||  |||  |  |  | |  |  |   | ||   |   | || | |    || |   |  | | ||||   |   |||   |  |||||||||||||| ||||| ||||| |||| ||||||||||||||||||||| || || ||||||||||| || || ||  | || ||||||||| ||||||
----aacttgtctacagtgggtgaagtttagttctagtagtagtagggccttttgcttgaacttggcatgtattgatagtctgatatgttgctttctatcacagGTGGTTGAGGTAAATGTGAAAGTTGAAAATGCAGGCACACATAATGTGCACAACAACGCTTTCTATGCCGAGGAAAAACTACTGAAATCTGAGCTGCAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G36130.1 (Glycine max), 3'ss of exon 3
taattaccactgcacattgcatgatatcaatctgtcttcatccaatggagatccctgtattccatattgaagccattgtgattgatcatttttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG
                                                       |||| | |  | ||    || | | | |  | |  | |  |  |||| || ||||| ||| | ||||| ||     ||||     | ||||| || |||||||| ||||||||||||||||  ||||||| |||||| ||| |||
----------------------------------------------------gtatgtaattctcagtg--ctcactcttactcctaagatgttttatagGTTGTGGAGGTCAATATCAAAGTCGAGGAACCAGGTGAGAAGAATGTTCACAATAATGCATTCTATGCTGAAGAGACCTTGCTCAGATCTGAATTGGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G18810.2 (Glycine max), 3'ss of exon 8
taattaccactgcacattgcatgatatcaatctgtcttcatccaatggag-atccctgtattccatattgaagc---cattgtgattgatc--atttttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG
   || | | | || ||||  ||| |    |   || |  ||||||  |  ||   |||| | | | |  |||    |||| | | |   |  |  | |  |  |||| || ||||| ||| | ||||| ||     ||||     | ||||| || |||||||| ||||||||||||||||  ||||||| |||||| ||| |||
--ttttcaagttca-attg--tga-acagcttcctccttctccaataaactatgtatgtaattcttttctaagtgcacattcttactctcccaagatgttttatagGTTGTGGAGGTCAATATGAAAGTCGAGGAACCAGGTGAGAAGAATGTTCACAATAATGCATTCTATGCTGAAGAGACTTTGCTCAGATCTGAATTGGAAG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 8
----taattaccactgcacattgcatgatatcaatctgtcttcatccaatggagatccctgtat-tccatattgaagccattgtgattgatcatttttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG
    |  || |   |   || |   |||||||| | |    | |   ||   |   || | ||| | || ||||| |    |    |||| |||||||  |  |||| |||||||| ||||||||||| |||    |||| |   ||||||| ||||| ||||| |||||||||||||||||  |||| |  |||||  ||||||
catcttttttcttttattcaatat-tgatatcattattcacttaaagaaaatattaccatatatgttcacattgatgatgat----ttgagcattttttctatagGTTGTTGAGGTCAATGTTAAAGTTGAAGAACCAGGGAAGAATAATGTTCATAACAATGCATTCTATGCTGAAGAGAAACTGCTTAGGTCTGAAATGCAAG

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|32919574|gb|CF024386.1|CF024386
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|211506668|gb|FL391689.1|FL391689
EST:     GACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: GACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|211134086|gb|FL422141.1|FL422141
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|50326819|gb|CO521945.1|CO521945
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|60342955|gb|DN209928.1|DN209928
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|67025362|gb|CO454111.1|CO454111
EST:     CCCGCATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|67028492|gb|CO457241.1|CO457241
EST:     CCCGTATGGACATGGCTGTTGATTGCAACCCTA-TGAAGCTCATAACCAG                         -TGGGTTGAG-TTA-TGTTTAAGTGGAA-GTGCAGGC-CACATA-TGTGCA
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGG-TTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCA
EST: gi|50326829|gb|CO521955.1|CO521955
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|67010284|gb|CO439033.1|CO439033
EST:     CCCGCATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|211466963|gb|FL423374.1|FL423374
EST:     TTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: TTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|31348944|gb|CD433301.1|CD433301
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
EST: gi|32831046|gb|CD970724.1|CD970724
EST:     CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAG                         GTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT
genomic: CCCGTATGGACATGGCTGTTGATTGCAAACCTAATGAAGCTCATAACCAGgttgggggtt ... tttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagatccctgtattccatattgaagccattgtgattgatcatttttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG
                                  gattgat  putative branch site (score: 4)
                                        tcatttttc  CT-rich tract
                                       atcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattaccactgcacattgcatgatatcaatctgtcttcatccaatggagatccctgtattccatattgaagccattgtgattgatcatttttcgtgcagGTGGTTGAGGTTAATGTTAAAGTGGAAAGTGCAGGCACACATAATGTGCATAATAATGCTTTCTATGCTGAAGAGAAGTTGCTCAAATCTGAGTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT