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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgcctttttatctcatctataattgctgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA

Basic information

species Zea mays
transcript GRMZM2G091151_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 3
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgcctttttatc----tcatctataattgctgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA
     |   | || | || ||    | ||   |    |  ||| | |   ||||  | |||||  | | |        |||  | |   ||||    | ||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||| |||| ||| | |||||||||||||| ||||||||||
---cattgcagatttcctattgcacctcaatatttgcaattctctctgctttgac-cattattatcctatggcagtagtcacttctctatgcttaaatttgcagGTTGGTCTAAACAACATCAAGGAGACAGATTTTGTGAATGTCACAATACAGTCATTAATGAGAATTACTCCTTTAAGAAATTTCTTTCTCATCCCTGAAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 4
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgcctttttatctcatctataattgctgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA
            |||||||||  | |  ||   |||         || |    | ||| |   |    |  |  | ||| ||  |        | | |||||||| ||||| || |||||||||||||||||||||||||| ||||| || ||  ||||||||||||| ||  |||||||||| ||||| ||||||||||
-----------gtatacttttcatgcctataaaaatg--------ttttggaaaggctgttaggggcctacaatttatccattgtattgtgacttttcagGTGGGACTTAATAATATCAAGGAGACTGATTTTGTGAATGTAACAATTCAATCCCTAATGAGAGTTACCCCCTTGAGAAATTTTTTTCTTATCCCTGAAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 4
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgcctttttatctcatctataattgc--tgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA
            |||| ||||  | |  || | ||| |  | |   | | |||||  |||        | |       ||| |||||   ||   | | |||||||| ||||| || |||||||||||||||||||||||||| ||||| || || |||||||||||||| ||  |||| ||||| ||||| ||||||||||
-----------gtatatttttcatgcttatagaaatgaaatttcgattt-ttgatattttggaaaggctattaggggcctacaattgtattgtgattttcagGTGGGACTTAATAATATCAAGGAGACTGATTTTGTGAATGTAACAATTCAATCCTTAATGAGAGTTACCCCCTTGAGGAATTTTTTTCTTATCCCTGAAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G22350.1 (Arabidopsis thaliana), 3'ss of exon 4
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgccttttta-tctcatctataattgctgctt-----tgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA
                               |||||    | | | | |  | |  ||| ||       ||| | ||  ||| |  |   ||||     | || |||||||  | ||||||||  |  |||| || ||||||||||| ||||| ||||| || ||||||||||| ||||| || |||||||| || || |||||||
-------------------------------gtaatcc--tttctctttgattacacttgatcttgaaattaatgtctcctaaaggttaagcttgtaaatatgtagGTGGGGTTGAACAACATACAAAAGACAGAGTTTGTGAATGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGAATTTCTTCCTCATTCCTGAAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ30204 (Selaginella moellendorffii), 3'ss of exon 3
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgcctttttatctcatctataattgctgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA
            |  | | | | |  | ||||   ||  || ||  | || |||  |   |  |  | |  | ||  | | |    | ||||    | ||||||| |||||||| ||||||||||| || ||||| || |||| |||||||||  | ||| | || || || ||  |  | || || || || || || |
-----------gtg-agtgtcactcgagatggagttttagt-ttggtttactgacac---agggtttctgaagcttgtgtgt----ggtgct----gtagGTGGGGCTTAACAATATCAAGGAGACGGACTTTGTCAACGTCATAATACAGTCGCTCATGCGGGTGACTCCGCTCCGGGACTTTTTCCTGATACCAGAGA

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|211066153|gb|FL067272.1|FL067272
EST:     ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCNATTATCTACCTGGAATG                         GGGGGTCTTAACAACATCAAGGAGACTGATTTTTGTGAA
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTT-GTGAA
EST: gi|211066159|gb|FL067278.1|FL067278
EST:     ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG                         GTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGGCACAATACAG
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAG
EST: gi|211068893|gb|FL067282.1|FL067282
EST:     AAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGGAATG
genomic: AAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGG-AATG
EST: gi|211066145|gb|FL067264.1|FL067264
EST:     ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG                         GTGGGTCTTAACAACATCAAGGAGACTGATTTTGT
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGT
EST: gi|211066152|gb|FL067271.1|FL067271
EST:     ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG                         GTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAG
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAG
EST: gi|211066151|gb|FL067270.1|FL067270
EST:     ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG                         GNGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAG
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAG
EST: gi|211066150|gb|FL067269.1|FL067269
EST:     ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATG                         GTGGGTCTTAACAACATCAAGGAGACTGATTTT
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTT
EST: gi|211066157|gb|FL067276.1|FL067276
EST:     ATAAGCAGNGGTCTANAGCACTTGATGGCTCCAATTATCTACCTGGAATG                         GGGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCNCCATACAG
genomic: ATAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGAATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAG
EST: gi|211066156|gb|FL067275.1|FL067275
EST:     TAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGGGAATG                         GNGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACA
genomic: TAAGCAGTGGTCTAGAGCACTTGATGGCTCCAATTATCTACCTGG-AATGgtatgtatcc ... ctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctattgatgctttattgcctttttatctcatctataattgctgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA
   tattgat  putative branch site (score: 3)
                                          ctgcttt  putative PPT
                               atctataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctcaaaaatatacttttattacacatggtaattaggtctttttctattgatgctttattgcctttttatctcatctataattgctgctttgtgcagGTGGGTCTTAACAACATCAAGGAGACTGATTTTGTGAATGTCACAATACAGTCATTAATGAGAGTTACACCTCTGAGAAATTTCTTTCTAATCCCTGAAA

- - - -aaaaata
- - - - - - - - - - - - -cacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgctg