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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG

Basic information

species Zea mays
transcript GRMZM5G879882_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 8
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
||||||| ||   ||      || || |       || |||| ||| || ||     ||   || |||||   | | | | |       | |   |||||    |   | | |||| ||  |   | |||||||||||||||| ||||||||||||| |||||||||||| ||||||||||||||| ||||||||||||| || |||||||||||||| ||||||||||
gtaatttatgattacaagcgtttattttt------gcctgcaaagaagcatt----acaactcttttgatactgcacaatttttctattaaagaagtactgattt---tttctgtacattaaaactcagGTTATAGACAAGTCCTTTGGTTTTGATAGTGCTGTAGAAGAGGCCCAGCGTGCCATTGATGCAGCTCATGTTGAGGCTTCAAGTGCTGAGAATGGAATAG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 7
gtaatttttggccacttctacttgttctcttttcagcttgca-tagatgct--tttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
       |  ||    |  | |||  |   |     ||| || |||| |||  ||||||| |         || |  ||     |       | ||    ||     | |  || | | ||  |    | ||||||| || ||||||||||||||||| |||||||| ||||| || || || ||||| ||||| ||||||||||||||   |||  |||| ||||| || |
------gtgagcatgcttgaattggacatctgaagccttacaatagaagctactttgctgaa--------aatataaaaaggatttacttttaaactgtcacctaattaaccatgt-tgtacctg-aatcagGTTATTGATAAGTCATTTGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
--gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacct-gtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
   |  || ||  | |  ||   || || | | | |      |    ||  | |   |  |       |||  ||  ||       ||  || || |  |  | | | |||| | |   | | | |  ||||||||| ||||| || ||||||||||||||||| || || || || || ||||||||||||||||||||||| ||||||  ||||  ||| ||||| || |
gtatgcttgttcacaatgtcatatttttgtttctccctggaactctaatcttatcattaaaatatatctgaagtgttagttctctatgaggaaacttcatcatgttcggattgtct---tctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 8
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctg-catacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatgg-ttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
|||||  |     | || ||    |     | | |   |   || |   || ||||  |||||  |         | || |  ||   | ||   |||    |  | | | |   | | ||| ||  ||||||||| ||||||||| ||||||| || |||||||| ||||| || || || || || ||| | ||||||||||||||   ||| ||||| |||||||| |
gtaatgatgctttagttgtaaaattgtatatgtgaaaattgttatacttttatgctatcatactccaaaggaaaaaggatttgagattaaag---tgtcacctatttaatgtcattctgtatttgaattagGTTATTGACAAGTCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCTGAGAATGGAATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 7
gtaatttttggccacttctacttgttctcttttcagcttgca-tagatgct--tttgctgcatacctcttgatttgga-agactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
       |  ||    |  | |||  |         ||| || |||| |||  |||| ||   |  |    |    || | ||| |    |||  ||||         | |  || | | ||  |    | ||||||| || |||||||| |||||||| |||||||| ||||| || || || ||||| ||||| ||||||||||||||   |||  |||| ||||| || |
------gtaagcatgcttgaattggacatccgaagccttacaatagaagctactttgatgagaatgtaaaaacaacgatatacttttaaacagtcaccta------attaaccatgt-tgtacctg-aatcagGTTATCGATAAGTCATTCGGTTTTGACACTGCTGTTGAAGAGGCACAACGAGCCATAAATGCTGCTCATGTGGAAGCAGAAAGCACTGAGAATGGTATCG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 8
gtaatttttggccacttctacttgt-tctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcaga--gacctgtactatgctgattatttgtatatatatggtt-agGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
|||||  |     | || ||    | | | | |  |  ||||    || |||||    |||    || ||   | || |  | | |  ||    |  |||    |  | | | |   | | ||| || || ||||||| ||||| ||| ||||||| || |||||||| ||||| || || || || || ||| | ||||||||||||||   ||| || || |||||||| |
gtaatgatgctttagttgtaaaattgtatatgtggaaattgct---atacttttatgccatcgtactcgaaaggaaaaaaagaatttgagtttaaagtgtcacctatttaatgtcattctgtatttgatttagGTTATTGACAAATCAATTGGTTTCGACACTGCTGTTGAAGAGGCACAACGAGCAATCAATTCTGCTCATGTGGAAGCAGAAAGCGCGGAGAATGGAATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
--gtaatttttggccacttc-tacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
   |  || ||  | |  || || || || |   | |      |    ||  | |   |  |   |  ||||  ||   |       || ||| || |    | | | ||||   |   | | | |  ||||||||| ||||| || ||||||||||||||||| || || || || || ||||||||||||||||||||||| ||||||  ||||  ||| ||||| || |
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatttgaagtgttggttatctatgaagaaacttc--atgttcggattgcct---tctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT4G32840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatttttggccacttctac-ttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
          |  | | |||  || |  |  ||  ||  ||||         ||    |    ||| |  | |||     |     |||   | ||  | | || ||||  | | | |         ||||| || |||||||| ||||| ||||||||||| || || || || || ||||| ||||||||||| ||||| |||||  | ||||  ||||| || || |
----------gtaagtcctagattatcattattgtagtctgcactctcaaccttaac-ctcctctcctattctggttagtt----cgcaagaagct-caatttgatgatagtatctctg-----atctagGTCATTGACAAGTCCTTTGGATTTGATACTGCGGTTGAGGAGGCTCAACGTGCTATTAATGCAGCGCATGTTGAAGCGACCAGTGTGGAAAACGGCATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
                                      |   ||  |  || | |||| |      |   | | |   ||||| | |  |       |   ||   | |     | | ||| ||   |||| |||||||| || ||||| ||||| |||||||||||||| || || || || ||||||||||| |||||||||||    |||   || ||||| || |
-------------------------------------gtatgtatctctttctactgctttgtctcta--tagaagagctgtatttcttatgtggagaaattgagaacttgacttttgtatttgtgcagGTGATAGACAAATCTTTTGGGTTTGACACTGCTGTAGAAGAGGCTCAACGAGCTATTAATGCAGCACATGTGGAAGCCGAGAGTATAGAGAATGGTATCG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatt-----tgtatatatatggt-tagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
                          | ||| | || |   |    |  | | | |      ||||||||||   |    |  | | |  ||  |||   |   | || ||   |   || |  |  | ||||| ||      |  |||   ||||  ||||||| |||||||| ||||| ||||| |||||||| || || ||||| ||||| ||||||||||| ||||| ||| ||  ||||   || ||| | || |
gtacatctctttgtttccttaattgctgattataggaccggttggatattacacctgatttattgcatagata--taaattcaaaaacaatttttttcctattttttattgaccaattctctttttagttgatttttacctccgactattgctggtacagGTTATTGACAAGTCCTTTGGCTTTGACACTGCTGTTGAGGAGGCCCAACGTGCTATTAATGCAGCACATGTTGAATCTGAAAGTATCGAGAATTGTATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 8
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
||| || ||| | | | |  ||   |   ||||   |||   |  || ||||| |   | ||||     |     || ||||| ||       ||  ||  |   || |   |   | | |    | ||||||| ||||| || |||||||||||||||||||| |||||||| ||||||||||||||||| || ||||| ||| ||  ||||  ||| ||||| || |
gtacttcttgcctattgcacctgaattaattttgttcttttctccat-ctttttcaataaaccttgcatt-----agcctgtaatgt----gtcttcacctta--gactgcct---tctcttgattcagGTTATTGACAAATCGTTTGGTTTTGATACTGCTGTTGAAGAAGCACAGCGTGCCATTAATGCGGCACATGTTGAATCTGAAAGTATTGAGAATGGTATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 8
gtaa-tttttggccacttct---acttgttctcttttcagcttgcatagatgct---tttgctgcatacctcttgatttgga--agactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
|||  ||| || | | | ||      || | |   | || ||  |  |         ||   ||   |  |||| ||| |||  ||||| | |||  || |   | | |         |||||       || |  ||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| || || ||||| || ||||||||||||   |||  | | ||||| || |
gtaggtttctgacaaatccttgagtctgatattcgtgcaactctcgaaagaatcgaattgtatgatcaagtcttaattgggaccagact-ttgtgaggaaagacgaattg--------atttgacctggaattggcagGTTATAGACAAATCGTTTGGGTTTGATACAGCTGTTGAAGAAGCACAGCGCGCAATCAATGCTGCCCATGTGGAAGCTGAGAGTATTCACAATGGCATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------gtaatttttggccacttctacttgttctcttt-tcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
                                                                      |||| |||||  || | |    |       |  ||| |  |||   |  || ||     |   ||||||  |  |||  ||          |    || | ||  || | |  |||| |        |||| ||||| |||||||| || |||||||| || || |||||||| |||||||| || |||||||||||||||||||||   |||| | | |||||  | |
gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgattaattatgtattgt-tttcttgaagtccaagtgtgccaccgtctaatgcatatt-tgtcgaatgtg-gtatttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcat--acctcttgatttggaagactgtagtgcag---agacctgtactatgctgattatttg-tatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
|||  |||| | |||    | |      |      |  | |   | |  |||   || ||  |  | |     |    || |||||   |    | ||  |  ||     ||  || || |  |  | |||  |||| |||||||| ||||||||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||   |||| | | ||||| || |
gtacgttttagacacggaaattcaacaacacgatggaattctctgtt--tttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggc-agGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG

upper sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
--gtaatttttggccacttctacttgttctcttttcagcttgcatagatgctt-ttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
     ||   |   | || ||||    |  |        |  |||   ||||| || |  |||    | ||| ||       ||| | |    ||| ||| || |  ||   |||||| |  ||  |   || | || || ||||| ||||| ||||| |||||||| |||||||| || || || || ||||||||||||||||||||   |||| || | |||||  | |
gtactatacatcatccctactacacagtgacgcgctttttcacatgtgtgcttatttccacatgttgcctgaattcattcg-tgt-gcgttctgacttgttctcttttggg-atttgtttcaat--gaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG

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|14208413|gb|BG842091.1|BG842091
EST:     TACAAGTAGCTGTTGCTGGTATTCCCAAGACTATTGATAATGATATAGCG                         GTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGT
genomic: TACAAGTAGCTGTTGCTGGTATTCCCAAGACTATTGATAATGATATAGCGgtaatttttg ... atatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGT
EST: gi|87153557|gb|DY398346.1|DY398346
EST:     TACAAGTAGCTGTTGCTGGTATTCCCAAGACTATTGATAATGATATAGCG                         GTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGT
genomic: TACAAGTAGCTGTTGCTGGTATTCCCAAGACTATTGATAATGATATAGCGgtaatttttg ... atatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG
                           tgctgat  putative branch site (score: 3)
                                attatttgtatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcatacctcttgatttggaagactgtagtgcagagacctgtactatgctgattatttgtatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG