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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA

Basic information

species Zea mays
transcript GRMZM2G409265_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 8
gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
|||  |    | |||| |  |  || ||  || |  ||  || ||| |  | ||||   | |||         | |     ||||||||||||||||| ||||||||||||||||| || || |||||||| || || || ||||||||||||||||| ||||| ||  |||||||| |||| || ||||
gtatgcgcaaagcatataattcgcctattgttagttttttgt-agtgcaaagcctaacgtacta---------tttgatgatttgttaagGAGAAGCTTCCACCAACGGATTCAAGACTCAGGCCAGATCAGCGGCATCTAGAGAATGGGGAGTACGAAAAGGCTAACTCTGAAAAATTGCGCCTGGAGA

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G04340.2 (Glycine max), 3'ss of exon 9
------------------------------gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                              || |   |      |   | | |  ||||  |     |  ||||     || ||| |  || |   |   | ||  | |      | ||||||||||| ||||| |||||||| ||||||||||||||||| || || || ||||||||||| ||||||||||| |||   |||||||   |  | || |
gtataatgatgtattaaatcattattcgatgtgcgttttcttttttcttcttatgcatctctaattctttgtta-----tagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGATCAGCGGCATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAAAAACAAAGGTTGGAAA

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G41940.1 (Glycine max), 3'ss of exon 8
--------------------------gtacacatggaacataaatataacccatcattggacttccgtta--gttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                           |  | | | |    |  | | |   ||   | | ||    ||   |||  || | | |  || |   |   ||||  | |      | |||||||| || || || |||||||| ||||| |||||||||||||| || || ||||||||||| |||||||||||||||   || ||||   |  | || |
gtatataatgatgtattagatcattatttgatacgcattccacttcttatatatgcgtcgtctctaattgttgtttatagctttttctgatcccgggtatttg-atcacggattaaagGAGAAACTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAA

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G03420.1 (Glycine max), 3'ss of exon 10
---------------------gtacacatgg-aacataaatataacccatcat---tggacttccgttagttcttaacctataatgctaaggc-acatttctacccttttgttaa-gGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                         |  ||  |  |   ||   ||   | ||   ||    ||   | ||| || |    |  | || |  |    | | |   |     |||| ||||||||| || || |||||||| ||||| ||||||||||||||  | || |||||||||||                                      
gtatataatgatgtattagatcattatttgatagtacgcattccacttcttatatatgcgtctctaattgttgtttatagCTTTTTCTGATCCCGGGTATTTGATCACGGATTAAAGGAGAAGCTCCCGCCCACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAA-------------------------------------

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G14820.1 (Glycine max), 3'ss of exon 9
gtacacatggaacataaa--tataacccatcattggacttccgttag-ttctta---acctataatgctaaggcaca----tttctaccct-------tttgtt---------aagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
||| | |||    || ||   || |  |    |  |  |||| ||   ||||||   | || |||| ||  |  | |    |||||   |        |||| |         ||||||||||| ||||| |||||||| |||||||||||||| || || || || ||||||||||| ||||||||||| |||   || ||||   |  | || |
gtata-atgatgtattaaatcattattcgatgtgcgttttcctttttcttcttatgcatctctaattctttgttatagccttttctgatcccgggtaatttgatcacggattaaagGAGAAGCTTCCACCCACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAA

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT4G12460.2 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------gtacacatggaacataaatataacccatcattggacttccgttagttcttaacc-tataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA------
                                  ||| ||||| |   |   | |   |  |  ||| | |   |||  ||   |||  | | ||  |   | |  ||| | |||||   ||||||| |||||||| ||||| ||||| |||||  ||||||||||||| ||| ||||||| || || || |||||||| ||||  || ||||   |  | ||||      
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgtt--ttagcaactgtgtgatcttttcgtaattttgttcccttggtttaaggaaaagCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGAGAAGAC

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT4G12460.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------gtacacatggaacataaatataacccatcattggacttccgttagttcttaacc-tataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                                  ||| ||||| |   |   | |   |  |  ||| | |   |||  ||   |||  | | ||  |   | |  ||| | |||||   ||||||| |||||||| ||||| ||||| |||||  ||||||||||||| ||| ||||||| || || || |||||||| ||||  || ||||   |  | ||||
gtatattagtatttttttaattttggatttgtttgtaaacatgaattttgggtttctgctgtacttgaaatcttgtt--ttagcaactgtgtgatcttttcgtaattttgttcccttggtttaagGAAAAGCTGCCTCCAACAGATTCTAGGCTCCGACCAGATCAACGACACTTGGAGAACGGTGAATATGAGAAGGCAAATGAAGAGAAACAAAGATTAGAGA

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 7
------------------------gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggc-acatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                         |    |||   ||||   ||   ||     || |  ||   | ||  || |    |    || |  |    | | |   |     ||||||||||||| ||||| ||||||||||| || |||||||||||||| || || |||||||| || || || ||||| ||||| |||||||| ||  | ||||
gtagagataatgtattgaatcaatttttttatgtg-catattcattttcctcttatgcatatctaattgtcttttatagctctgtctgatcccgggtatttgatcacggattaagGAGAAGCTCCCACCCACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGA

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------gtacacatggaacataaatataacccatcattggac---ttccgttagt------tcttaacctataat---gctaaggcacattt----------ctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                                                    || | ||||    |   | |      |  ||       ||| |||| |      | | || |  ||     |  ||    ||| |           ||   | || |  |||| ||| ||||||| || ||||||||| ||||||| |||||| | || ||||||||||| || || ||    |||||| | ||||||||||| || ||  
gtgagtatctgcaattttcttagacttaaatgcttatactagagatttgacttatatatggctgttttttttctttttttcttttttcctttcagttaataagaaatatgaatcggtagacgagtcaacattcatctacttataaatttaatttattttgtagGAAAAGTTGCCACCTACAGATTCAAGGTTGAGACCTGATCAAAGACATCTGGAGAATGGTGAATATGATGCTGCCAATTCAGAAAAACTGCGACTTGAAC

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ15167 (Selaginella moellendorffii), 3'ss of exon 8
gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataat-gctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                                          |  |||  | | | || | ||| | |  | |            ||  ||||||||||||||||||| |||||  | |||||||| |||||||| ||  |||| || || || |||||| |||| ||| | ||||| |||||  | ||  
-----------------------------------------gtctttcaaagcatttattcgctcaagttc-tcatggtaaaagcgtgcagGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTGGAAG

upper sequence: GRMZM2G409265_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 9
gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
                        |  |||     | |   || |  || ||  | | ||| |||  | | |                ||||||||||||||||||| |||||  | |||||||| |||||||| ||  |||| || || || |||||| |||| ||| | ||||| |||||  | ||  
----------------------gtctttca--aagcatttattcg--ctcaagttctcatggtaaaacgcgtgc--------------agGAGAAGCTGCCACCAACAGATTCCCGACTGAGACCTGATCAACGACATTTGGAAAACGGTGAATACGAGCAGGCTAATTCCGAAAAGCTGCGGTTAGAAG

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|148943629|gb|EC888693.2|EC888693
EST:     ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAG                         GAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
genomic: ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAGgtacacatgg ... ttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
EST: gi|60346794|gb|DN213767.1|DN213767
EST:     ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAG                         GAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
genomic: ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAGgtacacatgg ... ttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
EST: gi|60344714|gb|DN211687.1|DN211687
EST:     ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAG                         GAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
genomic: ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAGgtacacatgg ... ttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
EST: gi|60344453|gb|DN211426.1|DN211426
EST:     ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAG                         GAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
genomic: ACTTGTCCACATTTGCAATAACATTAAATGAGTTAACACCAGAGCTCAAGgtacacatgg ... ttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
EST: gi|78113595|gb|DV531986.1|DV531986
EST:     AATAACATTAAATGAGTTAACACCAGAGCTCAAG                         GAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG
genomic: AATAACATTAAATGAGTTAACACCAGAGCTCAAGgtacacatgg ... ttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA
           tcttaac  putative branch site (score: 2)
                                    tttctacccttttgtt  putative PPT
                                             ttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacatggaacataaatataacccatcattggacttccgttagttcttaacctataatgctaaggcacatttctacccttttgttaagGAGAAGCTGCCACCAACGGATTCAAGGCTGAGACCAGATCAACGTCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGTCTCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG