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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgacaccgcgtcaacttaattccctcgttagcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC

Basic information

species Zea mays
transcript GRMZM2G433591_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 4
gtacgtgacac---cgcgtcaacttaattccctcgttagcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
||||||| |||   |    ||  |   |  | |  |||  || || |||||  |  || |||| || |||||| |||||    ||   | |||||||||||||||||| | |||||||||||||||||||| || || |||||||||||||| |||||||||||||||||||| || |||||||| |||||||
gtacgtggcaccaacattccatttccgtaactttatta--ttatggtatcaattgtgggtcat-gacgagcaattctttctacacatattcagGAAGACGACAAGGCCCGCCTGGTGCAGGAAACGGGGTTACAACTGAAGCAAATCAACAATTGGTTCATTAACCAACGCAAACGAAACTGGCATAGCAACC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
---------gtacgtgacaccgcgtcaacttaattccctcgttagcttct--gctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
           |  |||  |  |  ||    ||||      ||  | | |     || |      |||   | |  |     ||||   |   |  | ||||| || || |||||  |  |||||||||||||||| |||||||||||||| ||||| || ||||| || || ||| | ||| |||||||||| |||||||
aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaat-gttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
----gtacgtgaca--ccgcgtcaacttaattccctcgttagcttctgcta--tcaggttcggctcattgatgagcaactctttgctta---ctcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
    | || |   |  |  |  ||    ||||      ||  ||| | | |  | |   |    | |||  | | ||| |  ||  | |    |  | ||||| || || |||||  |  |||||||||||||||| |||||| ||||||| ||||| || ||||| || || ||| | ||| |||||||||| ||||  |
aaatgaacatagtaagctactacagaagaatttaacaattgactttttcaaaattaatattaaatgatttctca-caatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 4
------------gtacgtgacaccgcgtcaacttaattccctcgttagcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
             ||    | |       | ||    || | |    ||  |  |   |   |    ||  ||| ||| | |   |    ||  |  | |||||||| || ||||| ||  ||||||| ||||| ||||||||  ||||||| || || |||||||| || || ||| | ||| |||| ||||||||||| |
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgtt--ttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S77_59V6.1 (Physcomitrella patens), 3'ss of exon 5
gtacgtgac--accgcgtcaacttaattccctcgtta-gcttctgctatcaggttcggctcattgatgagcaactctttgctt---------actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
 | | | ||     |  ||  || ||| |     ||| |    | ||| ||  | |  |  |  |   || |||  |||| |          |  |   ||||| || || || |    | |  | ||||| || || ||| |||| |||||| ||||||||||||| || ||||| || ||||| |||||||| |||||||
-tgcataaccggtagactcttctgaatgcgtggcttatgacgtttctagcatat-catcaaaacgcccagtaacattttgttccgggacacaatgcaatcagGAGGATGAGAAAGAACAATTAATACAGGAGACAGGATTGGAGCTCAAGCAAGTCAACAACTGGTTTATAAACCAGCGAAAGCGAAACTGGCATAGCAACC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------gtacgtgacaccgcgtca--acttaattccctcgttagcttctgc-tatcaggttcg-gctcattgatgagcaact-ctttgc-ttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
                                                          ||  | ||      |||  | |  |||      |     | | | |||  |   |  ||| |||  |   |  ||  |||||  | |||  |||||| || || ||||   | ||| | ||||| || || ||| |  | |||||| | || || |||||||| ||||||||||||||||||||||||||||| |
gtatcaaaaaattcatcaggaatcctgaactacgtatatccattcatgctttatgttctagttcacgtaatttcagaattccatttatatatatatatatacgtattggtgacatgctgatttttccacctctgttttgcactcctcaaccagGAGGATGAAAAGGAGCGGCTGATTCAGGAGACAGGTTTGGAATTGAAGCAAGTGAATAATTGGTTCATAAACCAACGCAAGCGGAACTGGCACAGCAATC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ24870 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------------------------------------gtacgtgacaccgcgtcaacttaattccctcgttagcttctgcta--tcaggttcggctcattgatgag--caactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
                                                                 ||  |       |  ||||  ||          ||| |    |   | | | |    |  ||   |    | | | | | |    || |||||||||| ||||||||  | || || ||||| || || ||| |||| ||||| |||||||| ||||| || |||||  | ||||| |||||||||||||| |
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagattttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttatttttttttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ05363 (Selaginella moellendorffii), 3'ss of exon 4
gtacgtgacaccgcgtcaacttaattccctcgttagcttctgctatca-ggttcggctcattgatgagcaactctttgcttactcgtc-cagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
                               || || |   ||  ||   |    |||   | ||      | ||  |   |   ||  ||||| ||||| |||||  | ||||| || || || ||| || |||| ||||||||||||||||||||||| ||||| |||||||| |||||||||  | |||
-------------------------------gtgagttcacgcattctcagcattgctggatcatcgatctcactaggtagagatgtggcagGAGGACGAGAAGGCGCGGCTGGTCCAAGAGACCGGGCTGGAGCTCAAGCAAATCAACAACTGGTTCATCAACCAGCGCAAGCGCAACTGGCACCACCACC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------------------------------------gtacgtgacaccgcgtcaacttaattccctcgttagctt----ctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
                                                                 ||  ||      |  ||||  ||          ||| |      | |      |     |  ||      | | | | | |    || |||||||||| ||||||||  | || || ||||| || || ||| |||| ||||| |||||||| ||||| || |||||  | ||||| |||||||||||||| |
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC

upper sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ06200 (Selaginella moellendorffii), 3'ss of exon 4
gtacgtgacaccgcgtcaacttaattccctcgttagcttctgctatca-ggttcggctcattgatgagcaactctttgcttactcgtc-cagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
                               || || |   ||  ||   |    |||   | ||      | ||  |   |   ||  ||||| ||||| |||||  | ||||| || || || ||| || |||| ||||||||||||||||||||||| ||||| |||||||| |||||||||  | |||
-------------------------------gtgagttgacgcattctcagcattgctggatcatcgatctcactaggtagagatgtggcagGAGGACGAGAAGGCGCGGCTGGTCCAAGAGACCGGGCTGGAGCTCAAGCAAATCAACAACTGGTTCATCAACCAGCGCAAGCGCAACTGGCACCACCACC

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|78180499|gb|DV550872.1|DV550872
EST:     CTGTACTGAAAGCTTGGTGGCAAGCTCATTCGAAGTGGCCGTACCCAACT                         GAAGACGACAAGGCCAGGCTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAA
EST: gi|60346164|gb|DN213137.1|DN213137
EST:     CTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACT                         GAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAA
genomic: CTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAA
EST: gi|7844336|gb|AW787558.1|AW787558
EST:     CTGTACTGAAAGCTTGGTGGCAAGCTCATTCGAAGTGGCCGTACCCAACT                         GAAGACGACAAGGCCAGGCTGGTGCAGGAAACGGGATTGCAGCTAAAGCAG
genomic: CTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAA
EST: gi|211168938|gb|FL462174.1|FL462174
EST:     CTGTACTGAAAGCTTGGTGGCAASYTCATTCCAAGTGGCCGTACCCAACT                         GAAGACGACAAGSCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAA
genomic: CTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 120

AGAGATCATGCGCAAACGCAGGGCTGGGAAGCTTCCTGGAGATACCGCATCTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

AGAGATCATGCGCAAACGCAGGGCTGGGAAGCTTCCTGGAGATACCGCATCTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

AGAGATCATGCGCAAACGCAGGGCTGGGAAGCTTCCTGGAGATACCGCATCTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 94

AGAGATCATGCGCAAACGCAGGGCTGGGAAGCTTCCTGGAGATACCGCATCTGTACTGAAAGCTTGGTGGCAAGCTCATTCCAAGTGGCCGTACCCAACTgtacgtgaca ... actcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
                                        tgcttac  putative branch site (score: 94)
                                   ctctttgcttactc  CT-rich tract