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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA

Basic information

species Zea mays
transcript GRMZM2G101480_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 3
----------aaagtctatgctgttg----ttgtagtagttccattgatagctggga-agtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
           ||   ||   | ||     ||      ||| |||| |    |   | ||   || |  | |    |  |||     | | ||  || | || | | ||   |||||||||||||||||||| ||||||||||||||||| |||||||| || || ||||| |||||||||||||| || ||||| || ||||| || ||||| |
gtgccctgtccaaccatacaattttagaatttcctagcgttacattaacttttaccacagccactcgcacatacactaaccttcaactaaaatatgg-tgtgttttgcaa-acagATGATCAATGAGAAGCCCCAGGTGATCCAGGAGTACGAGTCAGGTAAAGCTATTCCGAACCAGCAGATCATCGGGAAGCTTGAAAGGGCTCTTGGAACAA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G42890.1 (Glycine max), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
        |  || |   || ||| |   || | |  ||    | |  | | ||   |  || | |  | |    |||| | ||    ||||  |||||| |||||||||||||||| || ||||||||||||||||||||||| ||||| ||||| ||||||||||| ||| ||||| | || || || || ||| | |
-------gtattgct--cgtcgta-tattatcggt--ctctttattttccttattagtatttaggcattatcaatgatgtgcat----tgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTATGAGTCAGGGAAGGCCATTCCAAACCAGCAGATAATTAGCAAGTTGGAAAGAGCTCTTGGAGCTA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G15420.1 (Glycine max), 3'ss of exon 3
-----aaagtctatgctgttg--ttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgag-gatatgg--tgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
         |||   |||| |  || |  |   |  |||  |   |          ||  |       | |  | |      ||| |  ||| ||   ||||  |||||| |||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| ||||||||||| ||||| ||| | || ||||| || ||| | |
gtattgctttcttctctgtagattttttttgaatatattattcattattggtctcttttttttcctactagtatttaggcatgatcaatgatgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGGAAGGCCATTCCAAACCAGCAGATAATTGGGAAGTTGGAAAGGGCTCTTGGAGCAA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G42900.1 (Glycine max), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttg--gttggcctctttatgagatgag-gatatgg--tgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
    |   |     |   |||| | |    || |||  |      |  ||| ||  ||    || ||   |       || |  ||  ||   ||||  |||||| |||||||||||||||| || |||||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||| | || || ||||| ||| | |
-gtattactctcccttcagtagaattatttttaatatatcatcgatctctttatttttcttattagcaattaggcattatcaatgacgtgcattgttacttgcagCTGATCAATGAGAAGCCTCAAGTGATCCAGGAGTACGAGTCAGGAAAGGCCATTCCAAACCAGCAGATAATTGGCAAGTTGGAAAGAGCCCTTGGAGCTA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G42680.1 (Arabidopsis thaliana), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
      |||  | |  || |      || ||   |  ||    | || | |  |   |   | |  || | |  |  ||    | |    ||   || |||| ||||||||||||||||| ||||| || ||||||||||| ||||| || || ||||||||||| ||| ||   ||||| ||||| || || ||| | |
-----gtatattatccttct-----ctctatatgtcccttattattaccctattttgtaactcggttcatgacaaagtgtt--tgtttctttttgtgtagATCATCAATGAGAAGCCACAAGTGATTCAAGAGTATGAGTCTGGCAAAGCTATACCCAACCAGCAAATCCTTTCTAAGCTGGAGAGAGCGCTTGGAGCTA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G58680.1 (Arabidopsis thaliana), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctcttta------tgagatgaggatatggtgttca---ttgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
                     ||| || ||||  |  |||  |  |  ||   || ||   || | |   |       |||  | |   |||||  ||      || || ||||||||||||||||||| |||||||| || || ||||| || || |||||||| || || |||||| ||   ||||| |||||||| || ||  | |
---------------------gtactttcatttttctctgt-atctttctctttcttttactgtctttcgtcagtaattgaattcattgtatgggttttgattctgtagCTGATCAATGAGAAGCCACAAGTGATCCAAGAATACGAGTCTGGGAAAGCAATTCCGAATCAACAGATCCTTTCAAAGCTGGAGAGGGCACTTGGTGCTA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0014g01260.t01 (Vitis vinifera), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
    ||| | ||  | ||      | ||  ||  ||| | | |  ||   | ||      |||  |               | | |  | ||  ||||||||||| ||||||||||| || ||||| || |||||||||||||| || || ||||| || || ||||| ||   ||| || || ||||| || ||   ||
-gtatctctccttctttttgtccggctctgttcctagttcgtacttaatctaatatcactttgatc---------------gttgttatatt--ttgcagATGATTAATGAGAAGCCCCAAGTGATACAAGAGTATGAGTCAGGAAAAGCCATTCCAAATCAACAGATAATCACCAAACTGGAAAGGGCTCTTGGTGTGA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: EDP07421 (Chlamydomonas reinhardtii), 3'ss of exon 4
--aaagtctatgctgttgttgtagtagttccat-tgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
  |       |  |   | | | |     | ||     | |   | | |      || | |||    || |||     | |           |  |    |||   ||||| |||||||| ||||||||||||||||| |||   |||||||| || |||||||  ||| |  |    |||||     | || || ||   | 
taattactggtagtaaagctttcgcgccgcaatgccgcaacgatgtactcagcacatgcctggaaaaccccttct---gctccctgcgccccgcaccccacagGCTATCAACGAGAAGCCGCAGGTGATCCAGGAGTACGAGCAGGGCAAGGCCATCCCCAACCCCCAGGTGCTCTCGAAGCTGTCCCGTGCGCTCGGCGTGG

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S35_215V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------aaagtct-atgct-gttgttgtag----tagttccattgatagctgggaagta-gcttgatccttgg--ttggcctctttatgagatga-ggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
                                                                        | ||| || |  ||||| ||      | | |   ||  ||  || | ||   || | |  |  |   ||||      |   || | |  | |||  | ||  |||||| | || ||||| ||||||||  |  | || ||||| |||||||| || |||||||||||||| ||||||||    ||  | ||  | |  || || ||||
gttttcccgcacttcttttatacaatcaaattgttggcagtatagaattcgcaatatttgacaccaggacggaatctgataccagttgtagtcacttctgggtattttattaagtgtgcagcgtgcattacacaggcatttggtggtcctcgaagcttacagttatcttttttcttgcagCTCATAAATGAAAAGCCACAAATTGTACAAGAGTACGAGTCAGGGAAAGCAATTCCCAACCAACAGATCATATCGAAATTGGAACGTGTGCTTGGTACGA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ33541 (Selaginella moellendorffii), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
                        |||    |||| | |     |    ||  |  |||| ||   | |||      |  |       || |   | ||| ||||||| |||||||| ||||| ||||| |||||||| || || || || || |||||||||||||||||   |||||||||| | || |||||| | |
------------------------gtttggatgattgattctttggttttttctttttggctgatttgttttccttgttggt-----ttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCGGGAAAAGCCATCCCCAACCAGCAGATCATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA

upper sequence: GRMZM2G101480_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36890 (Selaginella moellendorffii), 3'ss of exon 3
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
                      | |    ||||||   | ||  ||  |||     |||| ||   | |||      |  |       || |   | ||| ||||||| |||||||| ||||| ||||| |||||||| || || || || || |||||||||||||| ||   |||||||||| | || |||||| | |
--------------------gtttggatgattgattctttggttgtgtctt----tttggctgatttgttttccttgttggt-----ttgcttggtccagCTGATCAACGAGAAGCCTCAGGTCATCCAAGAGTATGAATCTGGAAAAGCCATCCCCAACCAGCAGATAATCTCCAAGCTCGAGCGCGCGCTGGGAGCCA

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|18650202|gb|BM499021.1|BM499021
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|113701251|gb|EE678755.1|EE678755
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|74239907|gb|DT647821.1|DT647821
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|5706204|gb|AI941980.1|AI941980
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAA
EST: gi|134768994|gb|DY742729.1|DY742729
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAGTGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|32921064|gb|CF025876.1|CF025876
EST:     TCATGCAAGCAAGGCTAGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGTAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|6342630|gb|AW165454.1|AW165454
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|93013854|gb|EB639374.1|EB639374
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|93013855|gb|EB639375.1|EB639375
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|24934216|gb|CA452434.1|CA452434
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
EST: gi|16927526|gb|BM080595.1|BM080595
EST:     TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAG                         ATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA
genomic: TCATGCAAGCAAGGCTCGATAAGAAGTTGACCCAGGCACAGCTTGCTCAGgtatttctgt ... ttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA
  gcttgat  putative branch site (score: 5)
                     tctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagtctatgctgttgttgtagtagttccattgatagctgggaagtagcttgatccttggttggcctctttatgagatgaggatatggtgttcattgcagATGATCAATGAGAAGCCACAGGTGATCCAGGAGTATGAGTCAGGCAAGGCAATTCCCAACCAGCAGATCATTGGCAAGCTCGAGAGGGCCCTGGGAACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG