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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC

Basic information

species Zea mays
transcript GRMZM2G370332_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
gtatgtgacactacggcgacatata-attccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
||| ||| ||| |      ||| |   |  | |  | |  || || |||||  |  || ||||  | || | | |||||    |   || ||||||||||||||||| || ||||||||||||||||| || || || ||||| || ||||| |||||||| |||||||||||||| |||||||| |||||||
gtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcatgac-gagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
---gtatgtgacactacggcgacat----ataattccctcgtcaactttt--gctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
    ||    | | |   || ||      | ||||      |  || |||     || |      | |   |    ||    ||||   |  ||  | ||||| || || ||||||||  |||||||||||||||| ||||||||||||||||| || || ||||| ||||| ||| | ||  |||||||||| |||||||
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaat-gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
------gtatgtgacactacggcgacatataattccctcgtcaacttttgcta--tcagcttgggttcattgct---gatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
        ||   |  ||||  |   |   ||||      |  |||||| | |  | |   |    | ||| ||    ||  | ||||   |  ||  | ||||| || || ||||||||  |||||||||||||||| |||||| |||||||||| || || ||||| ||||| ||| | ||  |||||||||| ||||  |
aaatgaacatagtaagctactacagaag--aatttaacaattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaat-gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 4
--gtatgtgacactacggcgacatataat--------tccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcat-ccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
    | |||||  |        | ||| |        |||| |   | |     ||  |   |     |  || ||||   ||||    | | ||| |  ||||| || || |||||| |  ||||||||||||| ||||||||  ||||||||||||| || ||||| ||||| ||| | ||  |||| ||||||||||| |
tatcaagtgacctttttaaagtaaatattatctgctatcccacacaagccacatctcccttatcaatctttttactga---actcaaatcatgttcttgtcagGAGGAGGATAAGGCAAGGTTGGTGCAGGAAACTGGATTGCAATTAAAGCAGATTAATAATTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 4
--------gtatgtgacactacggcgac-atataat-tccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
         | | | |    |     || || |  | || | |  |  |     |   |   |     |  ||||||| | |   |    || ||  | |||||||| || |||||| |  ||||||| ||||| || |||||  ||||||||||||| |||||||| ||||| ||| | ||  |||| ||||||||||| |
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgtt--ttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------gtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgat----ccactc----tttgc-ttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
                                                     | |   |    |||       | |||||| |    |  | |   |||  |  | |||    |||||||    ||||      |||||  |  ||| |||||| || || ||||  || ||| | ||||| || || ||| |  | |||||  | || || |||||||| ||||||||||| ||||||||||||||||| |
gtatcaaaaaattcatcaggaatcctgaactacgtatatccattcatgctttatgttctagttcacgtaatttcagaattccatttatatatatatatatacgtattggtgacatgctgatttttccacctctgttttgcactcctcaaccagGAGGATGAAAAGGAGCGGCTGATTCAGGAGACAGGTTTGGAATTGAAGCAAGTGAATAATTGGTTCATAAACCAACGCAAGCGGAACTGGCACAGCAATC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ24870 (Selaginella moellendorffii), 3'ss of exon 4
--------------------------------------------------------------------gtatgtga--cactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
                                                                     | |  ||  ||| || |  | | | ||    |  |  | | |||    | |  ||   ||  | ||   || | | | | |   ||| |||||||||| ||||||||||| || || ||||| || |||||| |||| |||||||| ||||| ||||| || |||||  | || || |||||||||||||| |
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagattttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttatttt---tttttcgcct-tctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ05363 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtgacactacggcgacatataattccctcgtcaacttttgc--tatcagcttgggttcattgctgatc-cactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
                                 || |  |   ||  | ||||| | | |  ||    |||| ||||   |    ||    | |||| ||||| ||||| || ||||| || || || ||  || |||| ||||| || |||||||||||||||||||| ||||| || |||||||||  | |||
---------------------------------gtgagttcacgcattctcagcattgctggatcatcgatctcactaggtagagatgtggc-agGAGGACGAGAAGGCGCGGCTGGTCCAAGAGACCGGGCTGGAGCTCAAGCAAATCAACAACTGGTTCATCAACCAGCGCAAGCGCAACTGGCACCACCACC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------------------------------------------gtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
                                                                      ||  |   ||| || |  | | | ||    |  |  | | |||    | |  ||   ||| | ||   || | | | | |   ||| |||||||||| ||||||||||| || || ||||| || |||||| |||| |||||||| ||||| ||||| || |||||  | || || |||||||||||||| |
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttatttt---ttcttcgcct-tctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC

upper sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ06200 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtgacactacggcgacatataattccctcgtcaacttttgc--tatcagcttgggttcattgctgatc-cactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
                                 || |  |   ||  | ||||| | | |  ||    |||| ||||   |    ||    | |||| ||||| ||||| || ||||| || || || ||  || |||| ||||| || |||||||||||||||||||| ||||| || |||||||||  | |||
---------------------------------gtgagttgacgcattctcagcattgctggatcatcgatctcactaggtagagatgtggc-agGAGGACGAGAAGGCGCGGCTGGTCCAAGAGACCGGGCTGGAGCTCAAGCAAATCAACAACTGGTTCATCAACCAGCGCAAGCGCAACTGGCACCACCACC

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|71330383|gb|DR801947.1|DR801947
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|32868323|gb|CF008005.1|CF008005
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|71330382|gb|DR801946.1|DR801946
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|60397901|gb|DN230717.1|DN230717
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|93280940|gb|EB673204.1|EB673204
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|31611855|gb|CD568477.1|CD568477
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
EST: gi|32868033|gb|CF007715.1|CF007715
EST:     CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACT                         GAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTGCTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCATACCCAACTgtatgtgaca ... attcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
                         tgctgat  putative branch site (score: 3)
                                   ctctttgcttattc  putative PPT
                                           ttattcat  TA-rich tract