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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattgaagctcattgtgttcgtgtcgtcgttgctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT

Basic information

species Zea mays
transcript GRMZM2G167669_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167669_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g29770.1 (Oryza sativa), 3'ss of exon 1
ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaatt-----gaagctcattgtgttcgtgtcgtcgtt--gctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
       ||  | ||            ||  |      |||||    |       |         | | | | || |  ||   | | |    |      |    |||||||| |||| || ||||||||||||||||| ||||||||||||||||| | ||||||||||||||  || ||||| ||| ||||||||||||||||||
-------ttaaaaaaacggaagaagcattgatcaatggaaagagttcatattatgtctctccatggataaatatgattttggtatggattaattcaatggtggtcagGTGAACCTGACCGGCGGCTACTACGACGCCGGCGACAACGTCAAGTTCGGGTACCCGATGGCGTTCACGGTGACCCTGCTGGGCTGGAGCGCCGTCGAGT

upper sequence: GRMZM2G167669_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattg--aagctcattgtgttcgtgtcgtcgttgctgctc-catatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
                                                  |  |  |||  ||||  | |   | | |  |||  |   |  | |  | |    ||   |  |  |    ||    | | || || ||  | | | || ||||  | ||||  || || ||||||||||| ||||||||||| ||||||||  | || ||||| ||||||||| || |  ||   ||| | || || ||||
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaaattgaccttgacgatggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT

upper sequence: GRMZM2G167669_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ16113 (Selaginella moellendorffii), 3'ss of exon 1
ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattgaagctcattgtgttcgtgtcgtcgttgctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
             |  ||      |||| ||  ||  ||| |          |  ||     ||     | |||  |  ||| ||||||||       |||||||  | ||||| |||||||||||  | || |||||||||||||| || ||||||||||||||||   |||| || |||   |||||||  || || |
-----------gtaccttagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcg-attttcgctgctgctc-------agGTGAATCTCACGGGAGGCTACTACGATTCAGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

upper sequence: GRMZM2G167669_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattgaagctcattgtgttcgtgtcgtcgttgctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
             |   |      |||| ||  ||  ||| |          |  ||     ||     | |||  |  ||| ||||||||       |||||||  | ||||| |||||||||||  |||| |||||||||||||| || ||||||||||||||||   |||| || |||   |||||||  || || |
-----------gtaccatagaatcttttgctcgtttgaaatgtttttcttgtggtttacctttctagtcgatcg-attttcgctgctgctc-------agGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT

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|91867832|gb|EB399814.1|EB399814
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025099|gb|FL297065.1|FL297065
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211022646|gb|FL297050.1|FL297050
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211022652|gb|FL297056.1|FL297056
EST:     GAGTCAGGTGGCGCGGG-ACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025091|gb|FL297057.1|FL297057
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|94472152|gb|EB701110.1|EB701110
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025101|gb|FL297067.1|FL297067
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025095|gb|FL297061.1|FL297061
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025092|gb|FL297058.1|FL297058
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAANAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|71449159|gb|DR830209.1|DR830209
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|91051415|gb|EB161833.1|EB161833
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211022643|gb|FL297047.1|FL297047
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|78089480|gb|DV517854.1|DV517854
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|71302691|gb|DR787458.1|DR787458
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025093|gb|FL297059.1|FL297059
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025100|gb|FL297066.1|FL297066
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211022650|gb|FL297054.1|FL297054
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|50327992|gb|CO523118.1|CO523118
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|76918273|gb|DV167229.1|DV167229
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|76936408|gb|DV174712.1|DV174712
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|93015453|gb|EB640973.1|EB640973
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211022647|gb|FL297051.1|FL297051
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|91876854|gb|EB406811.1|EB406811
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCCACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCCAGTTCCGG
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTC-GG
EST: gi|211022651|gb|FL297055.1|FL297055
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|71448838|gb|DR829888.1|DR829888
EST:     GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: GAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
EST: gi|211025102|gb|FL297068.1|FL297068
EST:     AGTCAGGTGGCGCGGGGACTCCGGCGCTCACCGACRGCCAACCCGAAAAC                         GTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT
genomic: AGTCAGGTGGCGCGGGGACTC-GGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGT

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 3 RNA-Seq libraries.


Block sizes: 18 (upstream exon), 32 (downstream exon)
Score: 1

CATCCTCTTCTTCGAGGGGCAGCGGTCGGGGCGGCTGCCGGCAAACCAGAGAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT


Block sizes: 41 (upstream exon), 34 (downstream exon)
Score: 24

CATCCTCTTCTTCGAGGGGCAGCGGTCGGGGCGGCTGCCGGCAAACCAGAGAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 202

CATCCTCTTCTTCGAGGGGCAGCGGTCGGGGCGGCTGCCGGCAAACCAGAGAGTCAGGTGGCGCGGGGACTCGGCGCTCACCGACGGCCAACCCGAAAACgtgcactagc ... ccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggaagaattgaagctcattgtgttcgtgtcgtcgttgctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT
                                        ctgctcc  CT-rich tract
     aagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggacctttttgacaatttttttcttttttctttttcaaaaagaaagaaggaagaattgaagctcattgtgttcgtgtcgtcgttgctgctccatatgtagGTGAACTTGACGGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGTTTCCCGATGGCGTTCAGCGTCACCCTCCTGAGCTGGAGCGCCGTCGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgctg