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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcattcacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT

Basic information

species Zea mays
transcript GRMZM2G154165_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 18
gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcattcacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT
    |||  || ||      ||   |      |||| |||||   |   ||||   | |  | | ||| || ||| ||   |||| ||  ||||||| || ||||||||||| ||||||||| | ||||||||||| || ||||| |||||||||||||| ||||||||| |||||||  | 
---gttagcttctttctccttatcgg-----gattatcttaagtca-ccctgtt-ctgatttgatact-ataattattaa-cagGACTGGTTGGCTATCCCAGTGATGATATCAATAAGTTCTTGTGGATGGTTCGTATTGGAGGGGGTGTATTCCCTCACATAAAGGAACCAGATTATTTA

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 18
gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcattcacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT
    |||  || ||    ||||   |      |||| ||| ||  |   ||||   | |  | |  || || ||| ||   |||| ||  ||||||| || ||||||||||| ||||||||||| ||||||||||| || ||||| |||||||||||||| ||||||||| |||||||  | 
---gttaggttctttctctctattgg-----gattatctttattta-ccctgtt-ctgatttgatgct-ataattattaa-cagGACTGGTTGGCTATCCCAGTGATGATATCAATAAGTTCCTGTGGATGGTTCGTATTGGAGGGGGTGTATTCCCTCACATAAAGGAACCAGATTATTTA

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 16
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 18
gttattacatttttggcttctagaa--gcaaacaattaccttaatcaagtgctgtcattcacctaaaactgatgattctttt-tcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT
     ||  | |||||||  |   |  || | |   |   |||     |   | | |||| |    | | ||  ||  |||  | ||| |||||||| ||||| |||||||| || || ||||| || ||||||||||| || ||||| || || || || || ||||||||||| ||||| || 
----gtatgtgtttggctcatgacattgccatcttgtgtattatctctgaagtat-attctct--gatcggacaatcatttcattagGTCTTATTGGTTACCCTAGTGATGACATCAACAAGTTTCTGTGGATGGTTCGTATTGGAGGCGGCGTCTTTCCACATATAAAGGAAGCTGATTATCTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 18
gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcatt-cacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT
    ||   || || | |  |    | | |  ||     |||  || |    ||| | |||    |  || ||  |  |||||||| ||| |||| || || |||||||| |||||||||||||| ||||||||||| || ||||| || |||||||| || || | |||| | ||||| || 
---gttggtttcttagttgttttctg-agatcatcttgataaaaaaatataatcactacactctgatgtgctgcctacttttcagGTCTTGTTGGATATCCGAGTGATGACATTAATAAGTTCCTGTGGATGGTTCGCATAGGAGGGGGGGTATTCCCCCACATCAGGGAACCTGATTATCTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 16
lower sequence: Vv03s0088g00210.t01 (Vitis vinifera), 3'ss of exon 4
gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcatt-cacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT--
    ||   || || | |  |  | |  | ||  |   | ||  || |    ||| | |||    |  || ||  |  |||| ||| ||| |||| || || |||||||| |||||||||||||| ||||||||||| || ||||| || ||||||||||| || |||||| | ||||| ||   
---gttggtttcttagttgttttatgagatcatctcgataaaaaaaatataatcactacactctgatgtgctgcctagtttttagGTCTTGTTGGATATCCGAGTGATGACATTAATAAGTTCCTGTGGATGGTTCGCATAGGAGGGGGGGTATTCCCTCACATCAAGGAACCTGATTATCTGGT

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g01590.t01 (Vitis vinifera), 3'ss of exon 2
gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcatt-cacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT
    ||   || || | |  |    | | |  ||     |||  || |    ||| | |||    |  || ||  |  |||||||| ||| |||| || || |||||||| |||||||||||||| ||||||||||  || ||||  || ||||||||||| || |||||| | ||||| || 
---gttggtttcttagttgttttttg-agatcatcttgataaaaaaatataatcactacactctgatgtgctgcctacttttcagGTCTTGTTGGATATCCGAGTGATGACATTAATAAGTTCCTGTGGATGGTTCACATAGGAGTGGGGGTATTCCCTCACATCAAGGAACCTGATTATCTG

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|67014712|gb|CO443461.1|CO443461
EST:     GGAGATCTTCAATTCTTTAGATGTCAAATATGTGCTTGTTATCTTTGGAG                         GGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTC
genomic: GGAGATCTTCAATTCTTTAGATGTCAAATATGTGCTTGTTATCTTTGGAGgttattacat ... tctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaattaccttaatcaagtgctgtcattcacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT
                                   aactgat  putative branch site (score: 3)
                                            ttctttttc  putative PPT
                                           attcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattacatttttggcttctagaagcaaacaattaccttaatcaagtgctgtcattcacctaaaactgatgattctttttcagGGCTTATTGGCTACCCAAGTGATGATATTAATAAGTTCCTCTGGATGGTTCGAATCGGAGGTGGTGTATTCCCTCAAATAAAGGAAGCAGATTACCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT