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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC

Basic information

species Zea mays
transcript GRMZM2G178227_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g50850.1 (Oryza sativa), 3'ss of exon 10
-accagaaaatcaa-ggcacctttttcttttatgcttagtaagctcta---gcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
  |   |  ||    |||| | |||||   ||   ||    |  | ||      | |||   || | |     | |||| || ||||     ||  |||  |||||||||||| |||||||||||||||||||| ||||| ||||||||| ||||||||||||| ||||||||||| ||||| |||||||| |||||||| || |
agcttcagcattggtggcatcattttcccatacagttctagatatttacatatgattttaaattgttaacatatcttaattgctatg-----atttttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA06G13290.1 (Glycine max), 3'ss of exon 10
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagca-aatttgttttctgatgcat----ttttaactgtta--tggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
        || ||         |  ||  | |  |||  |  | | | | |   |  ||| ||   ||     |||| |   |||  |    | ||   |  |||||||||| |||||||||||||| || ||| | || |||||||||||  ||||||  || || ||||| || |||||||| ||||| ||||||||||| || |
-------gataaatctgttaactgattaaaagggtagggacttgttgtataggattctttatggctcacagtattttgatcattaaataatataatatgtatttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA04G41530.1 (Glycine max), 3'ss of exon 10
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgtttt---ctgatgcatttttaactgtta--tggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
      |||||     |||  ||       | |  | |  | | ||| |   || |||    || |     |||  |   |||  |    | ||   || |||||||||| |||||||||||||| || ||| | || |||||||||||  ||||||  || || ||||| || |||||||| ||||| ||||||||||| || |
----ataaatctgttgacccattaaaagggtacggactt-gttatagtaggattctttatggctcacaatatttggatcattaaataatataatatgtttttcagGAATTTAAGTGTGAGATATGCGGGAACTACAGTTATTGGGGGCGTCGGGCTTTCGAACGACATTTTAAAGAATGGCGCCATCAACATGGGATGCGGTGTC

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G06160.1 (Arabidopsis thaliana), 3'ss of exon 9
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
              | |  |  ||  ||||||        | | || ||||   |      ||| ||  || || |        ||| |   ||   ||||| || || || ||||||||||| ||| |||||||||||||  ||||||||| |||| | ||||| || |||||||| || || || || ||||| ||||
--------------gtatgtagtttatttatgagaccattgttgtatcaaa--ggaacatagattcacattaaattt-------cttgt-tattacgcagGAGTTTAAATGCGAGATATGTGGGAACTATAGCTATTGGGGAAGAAGGGCTTTTGAGAGACATTTTAAAGAATGGCGACACCAACACGGAATGCGTTGCC

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv16s0098g00320.t01 (Vitis vinifera), 3'ss of exon 10
-------accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
        | |    |  |||   || ||    ||||   |  |    |  | |  |||    | |   ||| | ||| ||     |  |  || |  |   |||||||||||||||||||||||||||| || || || || |||||||| ||||||| |||||| ||||| ||||||||||| ||||||||||| ||||| ||||
gctatgtgctaactgagaaagaagccattggagtttactttggggggacaattgtgaatagcctct---atggactttgaag----actgcttttttttaatttcagGAATTCAAGTGTGAGATATGTGGGAATCACAGTTACTGGGGGCGTAGGGCTTTTGAGCGGCATTTTAAGGAATGGCGCCATCAGCATGGTATGCGTTGCC

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S218_51V6.1 (Physcomitrella patens), 3'ss of exon 10
----accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctt-tgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
    ||          ||  |    ||||  || |||   ||| |    | ||  | | ||||||      |||  | |||  || |||   || |  | ||||||| || || ||||||||||| || ||  ||||||||||||| ||| |||||| ||| || || |||||||||||| | ||||||||||| ||||| ||  
taagacgcttggccgtagaaatgaatttcggttctgcagtgtagg----accatctcttttttctcgcagctttgcacctgg-attgacgagtgataattttcagGAGTTTAAATGTGAGATATGCGGCAATTATAGCTATTGGGGTCGACGGGCTTTTGAACGACACTTCAAGGAATGGAGACATCAGCATGGAATGCGTTGTT

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ22878 (Selaginella moellendorffii), 3'ss of exon 9
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
                                    ||||    |   |   |  || | |        || | ||  | |   | | || ||||  ||||| ||||| || |||||||||||||||   ||||| |||||||||||||| |  || || || ||||| |||||| | |||||||| || ||||| ||| 
------------------------------------gtaaaaagt--tatgctccttcttttgcaagccttcatctcctct---cctttgttttg--cagGAGTTCAAATGCGAGATATGTGGAAACTCCAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCT

upper sequence: GRMZM2G178227_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ30765 (Selaginella moellendorffii), 3'ss of exon 9
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgtt---cagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
                                            ||  || ||  | | ||  |   ||  |  | || ||   ||  | |||||||   ||||| ||||| || |||||||||||||||  |||||| |||||||||||||| |  || || || ||||| |||||| | |||||||| || ||||| ||| 
-------------------------------------------gtaaaaagttattctcct--tcttttgctggccgtcatctcctc-tcctttgttttgcagGAGTTCAAATGCGAGATATGTGGAAACTCTAGCTACTGGGGGCGAAGGGCCTTCGAACGACACTTCAAAGAATGGAGGCATCAGCACGGCATGCGCTGCT

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|6021114|gb|AW066042.1|AW066042
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|21395072|gb|BQ539502.1|BQ539502
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|8102853|gb|AW927533.1|AW927533
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|6012339|gb|AW061695.1|AW061695
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|4966996|gb|AI691781.1|AI691781
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTTAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|78544608|gb|DV622106.1|DV622106
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|211201057|gb|FL359984.1|FL359984
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|211525491|gb|FL328378.1|FL328378
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|5058841|gb|AI737317.1|AI737317
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|24766537|gb|CA401687.1|CA401687
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAACCCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|31358406|gb|CD442763.1|CD442763
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGGCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAAC
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAAC
EST: gi|211500086|gb|FL310138.1|FL310138
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|78087328|gb|DV515721.1|DV515721
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|67024526|gb|CO453275.1|CO453275
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|9742728|gb|BE518876.1|BE518876
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|8102852|gb|AW927532.1|AW927532
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|76290493|gb|DV030061.1|DV030061
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|211386010|gb|FL329694.1|FL329694
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATMTGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|211024196|gb|FL472245.1|FL472245
EST:     TGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: TGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
EST: gi|60396481|gb|DN229350.1|DN229350
EST:     ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAG                         GAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT
genomic: ATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagtt ... ctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC
                       ttttaac  putative branch site (score: 2)
                                             ctttgttc  putative PPT
                     atttttaactgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accagaaaatcaaggcacctttttcttttatgcttagtaagctctagcaaatttgttttctgatgcatttttaactgttatggacttatgctttgttcagGAATTCAAGTGTGAGATATGTGGAAACCATAGCTATTGGGGGCGAAGGGCTTATGAGCGTCATTTCAAGGAATGGCGTCATCAGCATGGGATGCGATGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-ccagaaaa
- - - - - - - gcacctt
- - - - - - - - - - - - - - -atgctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatt