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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

Basic information

species Zea mays
transcript GRMZM2G127948_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g06980.2 (Oryza sativa), 3'ss of exon 2
gtatgttccgctttcccgggccgatctctcgg-cggcgacctagctgctggacagatcga--------gatctgaaaaaatgg--------cgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
||| |   ||  | |||    |   |||| || |  |||    |     ||  | |||||        |||  | |   || |        | |||||||||||||||||||| || || ||||||||||| ||||||||| ||||  | ||||||||||||||||||||||||||||||||||||||||||||||||
gtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatcgatttgattcgattgggagggatcgatgttgttcttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 2
------------------------------------gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctgg--acagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
                                      || ||      |        |||   |    ||   |   |||  |||  || |||       ||||||||   |   ||||||| | ||||| ||||| || ||||| ||||||||| ||||||||||| | |||||||||   |||||||| |||||||| || || |||||||| || 
gtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtt--tggtttctctgctcgtggttactgattttttgttgaaaaaaaaaca-acagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G11530.1 (Glycine max), 3'ss of exon 2
-----------------------------gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctgg--acagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
                               |  ||  |  | |          ||      ||   |   |||  |||  || |||     |     ||||       ||||||| | ||||| ||||| || ||||| ||||| ||| ||||||||||| | |||||||||   |||||||| |||||||| || || |||||||| || 
gtatatatataactatttcatttttcaattgacattttgactcctatttatatgcttcgtttggtttctctgctcatggttactgattttttttgttgaaaacaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAATTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGA

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 2
---------gtatgttccgctttcccgggcc---gatctctcggcggcgacctagc---tgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
            || | ||  ||| |    |   ||   | ||  | | |  |      || | |  |  |     |  |    ||       ||||||| | ||||| || || || || || ||||||||| ||||||||||  |||||||||||   |||||||| ||||||||||| ||||||||||| |||
gtgagcttttcttgattcggattctcaaatctttgaatacccgttgtctatttgatgcttgtttgtaacgttagtgttggtttgaaaacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGC

upper sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 2
-----------gtatgttccgctttcccgggccgatctctcggcggc-------gaccta---gctgctggacagatcgagatctgaaaa--aatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
           |  |  | |    ||   | | ||  ||     ||        || | |   | || |||    |  |     | | ||  ||||  |  ||||||| | ||||||||||| || || || ||||||||| ||||||||||  |||| ||||||  ||||||||| |||||||| |||||||| |||||||||
gtgagagatgagattcattcaacctctgtgtctgaattcatactggattaatgggatcaataggatgatggttttaatggagcttaagaattaatgatg-acagGAACATCATGACGACCTCGGCTGATGAAGGGCAGTTCTTGAACATGCTGCTCAAACTCATCAACGCCAAGAACACCATGGAAATCGGCGTTTACACCGGC

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|18659584|gb|BM500414.1|BM500414
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|211221107|gb|FL365189.1|FL365189
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|211388332|gb|FL320898.1|FL320898
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGGTCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|211460076|gb|FL334958.1|FL334958
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCANG                         GAACCTGAGTGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCA
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGA-TGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCA
EST: gi|211015370|gb|FL327151.1|FL327151
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|211359692|gb|FL340690.1|FL340690
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCRAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|211200543|gb|FL334723.1|FL334723
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCRAGGTCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|149076214|gb|EE164811.2|EE164811
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|148967413|gb|EE018639.2|EE018639
EST:     AGCCGGAGAGCATGAAGGATCTCCGCGAGATCACCGCCCAAGCACCCATG                         GAACCTGATGACCACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCCT
genomic: AGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCC-AAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|74233832|gb|DT641746.1|DT641746
EST:     GCCGGAGAGCATGAAGGAGCTCCGCNGAGATCATCCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GCCGGAGAGCATGAAGGAGCTCCGC-GAGATCA-CCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
EST: gi|211147965|gb|FL321980.1|FL321980
EST:     GAGCCGGAGAGCATGAAGGAGCTCCGCGAGGTCACCGCCAAGCACCCATG                         GAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT
genomic: GAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 176

TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 713

TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 681

TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1329

TACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGgtatgttccg ... tggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcggcggcgacctagctgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
                                     tgaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctggacagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC