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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA

Basic information

species Zea mays
transcript GRMZM2G117900_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 5
---aaaatg--gttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctcct-tgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
   ||||||   | || | || |||||| |     || |       ||  |  |||    |  | | |  ||| |   |   | | ||||||| |||| | || |||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||  | ||| |||| ||||||||||||||||| ||||| || ||||
tgtaaaatgctatcatttcaacttcttttatgggccactaa-----gactaggtattg-gtttacatttgttgaagcctgagaaattacctatttcctcttaacagGGACACGATATTCTCATGGCTACGATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTCTGATAGCAGCAAATGAAAGTTGCCCACAACCCCAGA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 5
--aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctcct-tgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
    |  ||| |    |  || |||   ||||  |||||| |     | | |  |   |||||||| ||  || | | |   |||||||| || | | || |||| || ||||||||||||||||||||||||||||||||||||||||||||||||||  | |||||||| ||||| |||||||| || ||||| || || |
ttttatgggtcactgcatattgttttttattt--tttgatctctcgaagtcaataatgagaaaata-ttacatatgtaatacatacctatttcttcttaacagGGGCATGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCATTGCTTTTGATAGCAGCCAATGAAAGCTGCCCACAACCCCAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G18240.1 (Glycine max), 3'ss of exon 5
---aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataatt-gtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
    | ||  ||||    ||   ||| | |      |   ||  | ||    || | ||   |||| ||| || |||||  ||  | || || ||      |||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||  | ||  | || || || |||||||| || ||||| || || |
ttccatatttttatgagtatcctttttataagcaggtaattacaggtctccaatcaaatgctaaatcatttgtttgtttttacttttccaatttct----gtagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCGTTGCTACTCATAGCTGCTAATGAAAGCTGCCCACAACCACAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 5
-aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattg---tatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
  || |     |||| | |    ||  |  |||||  | ||  ||   || || | |   |  |   ||   | |||||  ||  | || || ||       ||||||| || ||||| ||||||||||||||||||||||| || ||||||||||||||| | ||  | || || || |||||||| || ||||| || || |
ataattacaggtcttcaatcaaatgctaaatcattgaacatatattttttttgttttgacatctgtgtgatatttgtttttacttttccaatttct----gcagGGACATGATATTCTTATGGCTACAATGCTTAATGGAGCAGCAATCATGGATGGAGCTTTGCTACTCATTGCTGCCAATGAAAGCTGCCCACAACCACAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT2G18720.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaatggttatcttaatttctttgacatttcatttgatattgatc--aattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
                    | | | ||    ||| | | |  |   || | |  | ||   | |   | ||||||       |   |      |||| ||||||||||| || || ||||| |||||||| |||||||| || || |||||||| ||| | ||  | || || || ||||| |  |||||||| || || |
-------------------gtataaaatgagttttaacactatttctaaatcttttgtaaccattttctatatgttaatgaggtgttttgtgtgttgattagGGACACGATATCCTAATGGCGACAATGCTGAATGGAGCAGCGATTATGGATGGTGCTTTACTAATCATTGCTGCGAATGAGACATGTCCACAACCACAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 5
-----aaaatggttatcttaat-ttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
     |   | | |     | | ||| ||||  ||||       ||   |   || |  |||    | |   |   ||||  |   || | | |    ||    |||| ||||| ||||||||||| ||||||||||||||||| || ||||||||||| || || ||||| ||||| |||||||||| ||||||||| || || |
gagtgagggttgatggagaagtattcattgatgtttc------catcttttgcttttcttatctctacttcattcttgttgaatgtattcttgttctattcttcagGGTCACGATATTCTCATGGCAACAATGCTTAATGGAGCAGCCATCATGGATGGTGCACTACTTTTAATCGCTGCAAATGAAACTTGTCCACAACCACAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 5
--aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
  |||    | |  ||||  |  | ||  |      | ||||   |   | |   |  || |||   || |||||||      |    || |       ||||| || || ||||||||||||||||||||||||||||| || || |||||||| ||  | ||| | || || || || ||||| ||||||||||| || |
ctaaagacttgactttaaggttctggatgtccaggcttatatgcctggttgagagtccagtaaagttttttatgtttt--tctttttcatttttcaatctagGGTCATGATATTCTCATGGCTACAATGCTTAATGGAGCAGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAACGAAAGCTGTCCACAGCCGCAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 4
aaaatggttatcttaatttctttgacatttcatttgatattgatcaat-tatgatatagaaaataattgtatgt-ttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
   | |||    ||||  |  | ||  |        | ||   |   | ||   | |||  | |  || | | | ||   |  |    |||| |     ||||| || || ||||||||||||||||||||||||||||| || || |||||||| ||  | ||| | || || || |||||||| ||||||||||| || |
--gaaggtggctttaagattctggatgtccaggcctaaatgcctgggtctactgtctagtgattttttttttatgtttttcttttttcatcttcccatctagGGGCATGATATTCTCATGGCTACAATGCTTAATGGAGCGGCAATTATGGATGGGGCATTACTTCTTATAGCTGCCAATGAAAGCTGTCCACAGCCGCAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 3'ss of exon 4
----aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
      | |    |  | | ||  | |||    | ||  ||    |  |  |  || | | |    ||||     |  |  | |||   | | |   |    |||||||||| |||||||||||||| |||||||||||||||||||| |||||||| ||| | |||||||| ||    ||||| ||||| || ||||| || |
aattcgactacacacatcacttaatctgagggcttatgggaagcggtactttcgtgttcttgtttttaatc---cggattga-aatgtttgtgtttgtttgcagGGACACGATATTCTCATGGCTACTATGCTTAATGGAGCTGCTATTATGGATGGTGCTTTACTTTTGATTGCCAGCAATGAGAGTTGCCCCCAGCCCCAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 3
aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
                                               | |     | | |  |     | | ||  | |  | | ||           ||||||| || |||||||||||||| ||||||||||| ||||| |||||||| || ||| | |||||||| ||    || ||||| || || ||||| || |
----------------------------------------------gtaagttcgtcgtagttttcgttttcttctagctgttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGCCCGCAGCCGCAAA

upper sequence: GRMZM2G117900_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 3
aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttc-aacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
                                                || | | |    | |  | || |  ||| | |  | | ||           ||||||| || |||||||||||||| ||||||||||| ||||| |||||||| || ||| | |||||||| ||    || ||||| ||||| ||||| || |
-----------------------------------------------gtaagttcttcgtagttttcgttttcttctagcttttcttacgaagactttcagGGACATGATATTCTCATGGCTACGATGCTTAATGGTGCTGCGATCATGGACGGCGCTTTGCTTTTGATTGCCAGCAACGAAAGCTGTCCGCAGCCGCAAA

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|211221672|gb|FL287024.1|FL287024
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|211221673|gb|FL287025.1|FL287025
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|32932475|gb|CF037287.1|CF037287
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|32935513|gb|CF040325.1|CF040325
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTGTCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|32944740|gb|CF049559.1|CF049559
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|148932915|gb|EE285716.2|EE285716
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|32945952|gb|CF050771.1|CF050771
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
EST: gi|148952113|gb|EC897906.2|EC897906
EST:     AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCG                         GGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT
genomic: AAAACACTAGAATGAAGCTCCTGAGACATGTTTCTTTTGTTGATTGCCCGgtatgataaa ... ccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA
                                      cctatctcctt  CT-rich tract
       atatagaaaataattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatggttatcttaatttctttgacatttcatttgatattgatcaattatgatatagaaaataattgtatgtttcaacaatacctatctccttgaatagGGACACGACATTCTCATGGCTACAATGCTTAATGGAGCTGCTATCATGGATGGAGCTCTTCTTTTGATCGCAGCAAATGAAAGTTGTCCACAGCCTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - tgacatt
- - - - - - - - - - - - - - -tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttca