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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

Basic information

species Zea mays
transcript GRMZM2G000645_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 15
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgc-ttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
||| |||| || ||||| |    |    || | |||        | |    | | ||  | |  |    |    |||  |||| | ||||   | | || | ||||||||||| || |||||||| |||||||||||||||||||||||||||||| | ||||| ||||| ||||||||||||||||||||||| || ||
gtatatattgtgtgctccatgcaagaatttttattt--------tgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
------------------------------------------gtaaatatagt-ctgctcgaaaacatttcttct----gtt--taaattctctatatgggcacttcatgt----catgacttcaattgcttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                                           ||  ||| |  ||  | |  | ||| | ||||    |||  | ||||   ||||||   | ||  ||     || |  |   |    |    | | |  |   | ||||   |  |||| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 15
--gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgctt-acatagt----tataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
   | ||     |   ||   | |  | |  | |    ||    | |  ||      || ||   |  ||    ||      ||||  |     ||||   ||||   |  |||| ||||| |||| ||||||||| ||||| |||||||||||||||||| |||| ||||||||||| |||||| | |||||||| ||||| ||
gtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4
------------------------------------------gtaaatatagtctgctcgaaaa-catttcttctgttt------aaattctctatatgggcacttcatgt----catgacttcaattgcttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                                           ||  ||| |    ||||  || ||| | |||| | |       ||||   ||||||   | ||  ||     || |  |   |    |    | |||  |   | ||||   |  |||| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 15
---gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcact--tcatgtcatgacttcaattgcttacatagttataagct--ttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
    ||| | |  ||   || | |    |  ||      ||    | |  ||      |  |      | ||     ||     |  | | || |   |  ||||   |  |||| ||||| |||| ||||||||| |||||||||||||||||||||||| |||| ||||||||||| |||||| | |||||||| ||||| ||
gtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatggg-cacttcatgtcatgacttcaattgcttacatagtt--ataagctttatac-ttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                       |   ||  | | ||  || |    | |   |  || ||||  |   ||   |||         ||   ||  | |  ||  |||||||| ||||||||||||||| |||| || ||||||||||||||||| ||| | || || |||||  | |||||| | |||||||| ||||| ||
---------------------gtaaggctcatttctaggtttttggaaagaaacgttttatgttttttattttgttgtaattgagattcagtactcctcttatattacagGTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
            | ||| | |   | | ||   ||  |||  ||| |||| ||  | |||   || |    |  |||| | |||  | |              ||||| || ||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||| || |||||  |  | ||||| || || ||
-----------gtactcaagagtctatttttatttctaatcatctttatgagc--tacattatataa---tagctgctaatatacctgtgg------------cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaaatatagtctgctcgaaaacatttcttctgtttaaatt-ctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                     |   | | | | | |   || ||||   | || | ||   || ||||  |  |||      || |||   | | |  || |   |||| || ||||||||||||||||| ||||| ||||| |||||||||||| |||| |  |||||||| ||||   |  | ||||| || || ||
-------------------gtattgtgcatatatgttggttactctgatttggaagtt---gttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 15
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtc-atgacttcaattgcttaca------tagttata-agctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
     ||| || |  | |   ||  || |  ||     ||| || ||||| |||  | || || ||  | |  ||| |||  |      | |||| | | |  |||  |  ||||| || ||||||| ||||||||| || |||||||| |||||||||||| | || || ||||| || || ||||| || ||||| ||||| ||
----gtattgtgta-ttgtccacccttgtcttgaaagtatt-tccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccatatgttc-cagGTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15
gtaaatatagtctgctcgaaaacatttcttct--gtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
             |    | |   ||  |||   |||  | |||| |||||  |  ||||||   | |  | || |    ||   | || | |   | ||  || ||||| || || |||| ||| ||||| || |||||||| ||||| |||||| |||| |  |||||||| ||||||||||| ||||| ||||| ||
-------------gtataagagagttgattccaggttgtatttctatatatatgatcttcattctaagg-tgcagtcatata---aattgttaatgtgatgatttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA

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|18965038|gb|BM661357.1|BM661357
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
EST: gi|19351531|gb|BM896063.1|BM896063
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
EST: gi|89106492|gb|DY576709.1|DY576709
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
EST: gi|22490520|gb|BU050443.1|BU050443
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                       tgcttac  putative branch site (score: 2)
                          ttacatagttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG