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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttgacagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT

Basic information

species Zea mays
transcript GRMZM2G044800_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g52354.1 (Oryza sativa), 3'ss of exon 3
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttga-cagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
  |  ||  |    || | |    | | || | |    ||   | | |  |  ||||| ||  | || |||| ||| | |||||      ||    | ||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttc-cagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 3
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttga-cagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
  |  ||  |    || | |    | | || | |    ||   | | |  |  ||||| ||  | || |||| ||| | |||||      ||    |  |||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||
ttgactagcaatttaaattcatctgaatattacagacctgagataaatgctactatttgttttaagtattgaacagttgattaactgcaattctttc-tagGGACATACATTGACAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCACAGTGCCAAGATGAACAGAACTAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g52361.1 (Oryza sativa), 3'ss of exon 3
gaggatatgatcccaagtactatggcacatgaa-aacattgcatttattagtgatatttcttgcatgtgttga-cagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
|    | |||     | |   |  |||  |||| ||   |   | | ||| || || ||||| || ||  ||| ||| | |||||| |    || |   ||||||| |||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||| |||||
gtatgtttgactagtaatttaaatgcagctgaataatgctatttctttta-tgctaattctttcaagtactgagcagttgattaat-tacaattccttgcagGGACATACATTGATAAGAAGTGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATCATTGCTGGAACATGCCATAGTGCTAAGATGAACAGGACTAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G11430.1 (Glycine max), 3'ss of exon 3
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttgacagatcattaatatttgtttgcc--cacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
    || | ||   || |    | ||  ||        ||  | |||    | |  |  ||  |  |   | |   | ||| ||  || |||      ||||| ||||||||||||||||| ||||| |||||||| | |||||| ||| | ||| | ||  | ||||| ||||| |||||||||||||||||||| |||||
--tcatttcatataaaatgtcctagctaatctctcttatgtgtatatggtcgtttctgtttctaaatcaggtcttttgatttattattcttttttaatacagGAACCTACATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATCCGTGGCCGTATCTTGGCTGGAACATGTCACAGTGCTAAGATGAACAGGACTAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G23400.2 (Glycine max), 3'ss of exon 3
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtg--ttgacagatca---ttaatatttgttt-gcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
    |  | ||  ||| |    | |    |     |  || |  | |  ||| |  ||  ||| | |         | |     ||| ||||  ||| |   ||||| ||||| ||||||||||| ||||| |||||||| | |||||| ||| | ||| | ||  | ||||| ||||| |||||||||||||||||||| |||||
----acttcatatcaaatgacctagttatttc--tctctgtacctgtatgtggtcatttctgcttttaaaccagttgttttgatttattattccttttgaatacagGAACCTATATTGACAAGAAGTGCCCCTTCACTGGCAATGTTTCCATCCGTGGCCGTATCTTGGCTGGAACATGTCACAGTGCTAAGATGAACAGGACTAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 3
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttgacagatcattaatatttgt-ttgccc---acagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
  | |||| |  |  ||| || |      |||  |  ||  |   |  |  || | ||   | |  ||||     ||| || |||| | | |||      |||||  | ||||||||||  ||||| |||||||||||||| ||||||||||||||  | ||  | ||||| || ||||||||||| |||||| | ||||| ||
-tgaatatca--ctgagtgctgtttgctttgattaggtttgaagcaaaaccgaaaatttgag-agatgttttgtaatctttgatatgtttattgtgtggaacagGAGCTTACATTGACAGTAAATGTCCATTCACTGGAACCGTTTCTATCAGAGGACGTATCTTAGCTGGTACTTGCCACAGTGCCAAGATGCAGAGAACCAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 3
-gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtg-atatttcttgcatgtgttgacagatcatta-atatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
    ||| |||      | |  | |   |||  ||||  |||||   |   |  |||  | |        ||  ||| | |||   ||||||| ||   |||||  | ||| |||||||||||||||| ||||||||||||||||| || |||||  | ||  | ||||| || ||||||||||| || ||| | || || ||
cactgatttgaatatgtg-atcaagcttcatagaaac-ctgcatcattctctatatacctttaagtcagattctcaggttattgtgtatttgtgtgga-acagGAGCTTACGTTGACAAGAAATGCCCCTTCACTGGAACTGTTTCCATTAGAGGTCGTATCTTAGCTGGTACTTGCCACAGTGCGAAAATGCAGAGGACCAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 3
gaggatat-gatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatg-tgttgacagat--cattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
|  || |   || |  |  | |||   |  ||   |  |    ||||   |      ||| ||   | || ||||   |  | ||  |  |||||||   ||||| || || ||||| ||||||||||| |||||||| ||||||||||| || ||| | ||  | ||||| || ||||| ||||| |||||||  || || ||
gttgacaccaattcagaaaagtattctaattggctagctaagctttaactgc----cttcatgagcgatgctgacttgttcccttcgttgttgtttggtaacagGTACTTATATTGATAAGAAATGCCCCTTCACTGGCACTGTTTCTATTAGGGGCCGCATCTTAGCTGGCACTTGCCATAGTGCCAAGATGATGAGGACCAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 3
-gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttgacagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
  |   ||   |   |   |  |     || |    ||   |      |       | || ||  | |    |   |  | |||  |||| |      |||| || ||||||||||||||||| || |||||||||  |||||||||||| ||| | ||| ||||||| || ||||||||||| |||||||  || || ||
gcaaagtagattttgagaaatcacaatgcaagcgcccaaatctgactctgtatgcttgtcatgtttataacaatgaactaataacttttgct-attggcagGAACATACATTGACAAGAAATGTCCGTTCACTGGAGGTGTTTCTATCAGGGGCCGTATTCTTGCTGGTACTTGCCACAGTGCGAAGATGATGAGGACCAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S30_89V6.1 (Physcomitrella patens), 3'ss of exon 3
-gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttgacagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
  | ||   || | || | |      |   |  || |   ||  |      | |||||         |  | | |     | ||    |  |  ||  |||| ||||||||||||||||| ||||||||||| |||  ||| || ||  | ||| | ||| |  | || ||     || |  | || ||||   | |||||
ttatgaacagagcgcaggcaggtgttcgggttcaacccaggctatgtgacttaatattctccatcattacttatat-ctgtgaactactcctctcctgcagGCACCTACATTGACAAGAAGTGCCCATTCACCGGAGATGTGTCCATTCGCGGCCGCATTCTCACCGGAACCGTGAACTGCACAAAAATGACTCGCACTAT

upper sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S21_269V6.1 (Physcomitrella patens), 3'ss of exon 3
gaggatatgatcccaagtactatgg--cacatgaaaacatt-gcatttattagtgatatttcttg-catgtgttgacagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
      ||| |   | |||  ||    | || |    |||| |  |||  |    || ||   ||   |||| ||| |  ||   | | ||  |   |   |||| ||||||||||||||||| ||||||||||| |||  ||| || ||  ||||| | ||  |  |||| ||     || |  | |||||||   | || ||
---ttcatgcttagacgtaaaataaatcccaaggttgcattagggtttgatgtgaatgttgagtgatctgtgctgagatctcgggagtgttc-taaactttcagGCACCTACATTGACAAGAAGTGCCCATTCACCGGAGATGTCTCCATTCGAGGCCGCATCCTAACTGGAACTGTGAACTGCACCAAGATGACTCGCACCAT

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|211021518|gb|FL120655.1|FL120655
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATCGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|149082096|gb|EE171275.2|EE171275
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAG                         GGACCTACATTGACAAGAAAATGCCCATTCACTGGAACTGTTTCTATCAAA
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAA-TGCCCATTCACTGGAACTGTTTCTATCAGA
EST: gi|32911263|gb|CF016075.1|CF016075
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATCGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|60337313|gb|DN204286.1|DN204286
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|211023959|gb|FL120673.1|FL120673
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATCGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|211023956|gb|FL120670.1|FL120670
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATCGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|211438278|gb|FL120651.1|FL120651
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATCGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|149004429|gb|EE039065.2|EE039065
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAG                         GGACCCTACATTGACAAGAAATGCCCCATTCACTGGAACTGTTTCTATCAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACC-TACATTGACAAGAAATGCCC-ATTCACTGGAACTGTTTCTATCAG
EST: gi|166572566|gb|EG286514.1|EG286514
EST:     AAGCAATCGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: AAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
EST: gi|148984955|gb|EE029619.2|EE029619
EST:     CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAG                         GGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG
genomic: CTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAAGgtataatagg ... ttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtgatatttcttgcatgtgttgacagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT
                                cattaat  putative branch site (score: 3)
                                        tttgttt  CT-rich tract
                              atcattaatatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggatatgatcccaagtactatggcacatgaaaacattgcatttattagtgatatttcttgcatgtgttgacagatcattaatatttgtttgcccacagGGACCTACATTGACAAGAAATGCCCATTCACTGGAACTGTTTCTATCAGAGGCAGAATTATTGCTGGGACATGCCACAGTGCTAAGATGAACAGAACTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG