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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT

Basic information

species Zea mays
transcript GRMZM2G106213_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatc---attctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattg-aagatttggctta---gcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
||| ||| |||||||||   || | |    |   |    | ||||| |  || ||    |||  | | || | |||| | | || |||    | | |  | || ||||||||||||  | || |  |||     | |  ||  || ||   ||||||||||||| || |  ||| ||  | ||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||
gtacgctatgctcttgaaacttgtag----catgtagggaatttttatccttctctcagttcatgctgtaggttttgtgaagtttggtatgtaaactgcagttacatcatttattgtgaaatgttacttctttacttaatttttactttgcatgtttgcttatgctgctaatgtatttgatagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATAGAGGCATTCTACAATGCCAACTTGGGGATAACCAAGAAACCTGTGCCAGATT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagta-gttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                              || | | |   |   | ||    ||||    ||| ||         || | ||||  |    ||   ||  || |  |     ||||||| | ||||    |  || || ||       | | |||| | ||||||||||||||| |||||||| ||||||||||| |||||||| ||||| || || |||||||||||  ||||||| ||||| |||||||| || || |
----------------------------------------------gtatgtgttccttctggtt----atttaa-tattacgaaaactttcttgtcattttcttgcatagcaaaatttagcatgcaattttttagaatgttgtatggcatgtttgtg-------tatattcaca-gGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggct--tagcctttttagtagt---------tgctatgttt---gcttatg------atgttgttgtgt-tcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
||     ||| |                                                                                                     || | ||   |  ||   |  |   | ||         ||| || |||   |  ||||      |||||  ||||| |  | |||||||||||||||| |||||||| ||||||||||| |||||||| || || || || |||||||||||  ||||||| ||||| |||||||| || || |
gtgattcctggtgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaactttcttgttattttcctgcatggtaaattagcatgcaattttttgagaatatgtacggcatgtttgtgtgtattcacagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATCGAGGCTTTCTATAATGCAAATCTGGGAATCACCAAAAAGCCTGTGCCTGACT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatga-tttgggcatttcggttgaaagattttaatttcatca-tttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
              ||||  ||  |  ||  | ||  | |  | | |||| |||  |  ||        | | |  |    ||  | |   | |||    |||| ||  || ||| || |   | |||  || |  || ||  || |    |||| |   || |  || |  |   |||||||||||||| |||||||||||||||||||||| ||||||||||| || ||||||||||| || ||  | ||||| |||||||| || || || ||||
-------------gtgagtgtttata-ttcatgtttacaacatctagtttgtattctgatgctcaagcaagtctctgttactctatggtttgctttcggattcaacagcttcttgtagct---gattatgctatgcagaag--gcaaaacctgctaactttgatcatgggcactgcagGTGCAAGCTTACCTATATGATGGTTACTGGGAAGACATTGGTACTATAGAGGCATTTTATAACGCTAATCTTGGAATCACCAAGAAACCAGTTCCTGATT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatt--tgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgt-tgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                                 ||||||   |||  ||| || |    | | | | |||| |||              ||  || ||||| |||  ||    |   |    | |   || ||  |    ||   |||||||||||||||| |||||||| ||||||||||| |||||||| ||||| || |||||||| || || ||||| || || |||||||| || || ||||
-----------------------------------------------------------------tatgatcactggaaattccgataatcaaaatgttattttatc--------------tgcatttgccttcttaagagaactttcatagagtcaaattgctgcataatctctgtagGTGCAAGCTTACTTGTATGATGGCTACTGGGAAGACATTGGTACAATTGAGGCTTTTTATAACGCTAATTTGGGGATCACAAAGAAGCCGGTGCCAGATT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgtt-caaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                                     |||| |       | || ||  |    |  ||      | ||     || || |||  | ||  ||        ||| ||  |  ||| |  |  |  ||   |  ||||||| || ||||||| |||||| ||||||||||||||||| ||||||||||| ||||| || |||||||| ||||| || |||||||| || || ||||
---------------------------------------------------------------------atttag---cgctgattaaagaagccgacctttcaacgtcatc----atatgccttt-cattcgtaactccaagtatcttgccaaatgctaatactaggtaatatcagGTGCAGGCCTACTTATTTGATGGCTACTGGGAAGATATTGGAACTATTGAAGCTTTTTACAACGCAAACTTAGGAATCACGAAGAAGCCCGTTCCTGATT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagatttta-atttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                                          |     |  | ||  |  ||  | |   | |||   |||| || |      |||   ||   |||  |  | |   ||   |   | ||||| |||| |  |||| |||||||| || || ||||| ||||||||||||||||| |||||||||||||| || ||||| ||  |||| || || ||||| ||||| || ||||
--------------------------------------------------------------------------gtagggtgagctgtgaatttccatacaacctcagccattggaggtaataaatagtagtt---gtacgtaatgttcctgagaagatttttgttctgtttatcagGTTCAAGCTTATTTGTACGATGGCTACTGGGAAGATATTGGAACTATTGAAGCATTCTACAATGCCAATCTGGGCATCACTAAGAAACCTGTTCCTGATT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S2_392V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                            | || |  |     |  || ||    |   |  | | |        || | ||   ||   |    || || ||   | |||          || |||     |||||| |   |||| ||||| ||||| |||||||| ||||||||||| || |||||||| || || || || || || || ||||| || ||||||||||| || || ||||
------------------------------------------------------------gaatattcgg---agatatctccaaaggttgtctgtgaacgtgatgttcagtggcaat---gacccgcattgttcccaattgta--------ttgtgactggattgtgtacc--agGTTCAAGCGTACTTGTATGATGGCTACTGGGAAGACATCGGTACTATCGAGGCTTTCTACAACGCGAATTTGGGCATCACCAAGAAGCCCGTGCCAGATT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S239_45V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                            | ||| |  | ||  | |    |||  |        ||| | | | |  ||||   ||   |   ||   ||||  |||     || |||| || | |     | || |||   |||| ||||| ||||| ||||| || ||||||||||||||||| ||||| ||||| || || ||||||||||| || || || ||||||||||| || || |
------------------------------------------------------------gtattgaaaactttcgta---aggtccactcccgaaaatgtgaccgtc-attggcaat---ggccagtacttttcctag---agatatttgattctaa----atcgtattcc--agGTTCAAGCCTACTTGTATGACGGCTACTGGGAAGATATTGGAACTATCGAAGCCTTCTACAATGCAAACTTAGGCATCACGAAGAAGCCTGTTCCTGACT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ16157 (Selaginella moellendorffii), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatg--tttgcttatgatgttgttgtgttca--aaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                                                                                     ||||  || || | |  ||   | |  | |    ||  |   |   |  | |||||     |||||||||| || || |||||||| ||||||||||| || || ||||| || ||||||||  |||| ||||| ||| | || |||||||| || ||  | |
--------------------------------------------------------------------------------------------------------------------gtttgtttttgc-tctgaagggatcgaaacgaacgtgacttaaacaatactctgttcgttgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

upper sequence: GRMZM2G106213_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17026 (Selaginella moellendorffii), 3'ss of exon 4
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatg--tttgcttatgatgttgttgtgttca--aaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
                                                                                                                     ||||  || || | |  ||   | |  | |    ||  |   |   || | |||||     |||||||||| || || |||||||| ||||||||||| || || ||||| || ||||||||  |||| ||||| ||| | || |||||||| || ||  | |
--------------------------------------------------------------------------------------------------------------------gtttgtttttgc-tctgaagggatcgaaacgaacgtgacttaaacaatgctctgttcgtcgcagGTGCAAGCGTATTTGTATGATGGATACTGGGAAGACATAGGGACTATAGAGGCATTTTACCATGCCAACTTAGGATTCACAAAGAAGCCCGTTCCAAACT

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|31356186|gb|CD440543.1|CD440543
EST:     ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
EST: gi|31357016|gb|CD441373.1|CD441373
EST:     AGGTTATTCCTGGCGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: AGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
EST: gi|32933002|gb|CF037814.1|CF037814
EST:     ATGACTTTGGAAGTGAGGTTATTCCTGGTGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTA
genomic: ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTA
EST: gi|463337|gb|T18304.1|T18304
EST:     ATGACTTTGGAAGTGAGGTTATTCCTGGTGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
EST: gi|67042108|gb|CO468363.1|CO468363
EST:     ATGACTTTGGAAGTGAGGTTATTCCTGGTGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
EST: gi|148950460|gb|EC896030.2|EC896030
EST:     CTTTGGAAGTGAGGTTATTCCTGGCGCACCAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: CTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
EST: gi|32856251|gb|CD995932.1|CD995932
EST:     ATGACTTTGGAAGTGAGGTTATTCCTGGTGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
EST: gi|211466744|gb|FL411592.1|FL411592
EST:     ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGG                         GTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA
genomic: ATGACTTTGGAAGTGAGGTTATTCCTGGCGCAACAGAAATTGGATTAAGGgtatgctctg ... tgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT
        tttttagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctctgctcttgagctttcttggtttctcttctccagtttttgtttttatcattctggatttatgatttgggcatttcggttgaaagattttaatttcatcatttattgaagatttggcttagcctttttagtagttgctatgtttgcttatgatgttgttgtgttcaaaagGTGCAAGCTTACTTATATGATGGTTACTGGGAAGATATTGGTACTATTGAAGCATTTTATAATGCAAACTTGGGAATAACCAAGAAGCCTGTACCGGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC