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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctctaattgctgtccgaagtccgctacacaattagacaagccggggtcaatttggtgagtttgctcgccggtggttcag

Basic information

species Zea mays
transcript GRMZM2G176029_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g39260.1 (Oryza sativa), 5'ss of exon 1
TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctctaa---ttgctgtccgaagtccgctacacaattagac----aagccggggtcaatttggtgagtttgctcgccggtggttcag---------------------------------------
 |||||| |||||||||| |  |||||||||||| ||||| ||||| ||||| ||||||||||| || ||||||  |||||||||||||||||| || |||||||| ||| || | |||      |  || ||       | ||    |||    |     ||| | ||  |||| ||    | ||||     | | ||| |                                       
GCGGCGGAGGGAGCATGGTGTCGCGCGTGGCCGTGCTCGCATTCTGCGTCGCCGGGATCTGGTCGGCGTACATCACCCAGGGCGTCCTCCAGGAAACCCTgtaagcgcccgcctccctccctccctccctctctctctctctctctctaatggtgctcgggagcggaggggaattgggc---tctgcttcggcgagtttctgaaaattgttcgccgttttctctccccgccgttcgttcag

upper sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G02330.1 (Glycine max), 5'ss of exon 1
TCGGCGGCGGGAGCATGGCGGGG-CGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctctaattgctgtccgaagtccgctacacaattagacaagccggggtcaatt-tggtgagttt-gctcgccggtggttcag-------
  |||    || | | |||   | ||| |    || ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| || ||||| | | ||||||   |||   |          || ||   ||  |||     | || || | ||||     ||||    ||| ||| | |      |  ||  |       
-AGGCTCATGGCGGAGGGCTCCGTCGCATCCTTGTGCTCGCCTTCTGCGTCGCCGGAATCTGGTCCGCGTACATCTACCAAGGCGTTCTTCAGGAAAATGTgtaagaatccctatccgctccgaaactctc--gagctcgcggtgaatttcgaaatgccgctactaattgctatgattttcgtttttttttttttttggtttcag

upper sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G05170.1 (Glycine max), 5'ss of exon 1
TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctctaattgctgtccgaagtccgctacacaattagacaagccggggtcaattt--ggtgagtttgctcgccggtggttcag-------------
  |    |||  ||  |    | || ||    || ||||||||||| ||||| || |||||||| || ||||||||||| ||||| || ||||| | | ||||||   ||    |     |     | ||   | | |||     | || || | ||||     ||||   | |  ||||  | |  | |  ||                
AGGCTCACGGCGGCGGGCTCCGCCGAGTCCTTGTTCTCGCCTTCTGCGTCGCTGGAATCTGGTCGGCATACATCTACCAAGGCGTTCTGCAGGAAAATGTgtaagaaaccgaatccgctcagaaattctc--gaattcgcggggaatttcgaaatgccgctactaattctcgctatgtttttttgttgatttttttttttttggttttag

upper sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT2G02810.1 (Arabidopsis thaliana), 5'ss of exon 1
TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctcta-attgctgtccgaagtc--cgctacacaattagacaagccggggtcaatttggtgagtttgctcgccggtggttcag----------------------------------------------------------------------------------------------
  | |   ||   |       | ||  |     |  | || || ||| || | |||||||||||||||||||||||||| ||||| || || |||||||||||||               | || | |   ||  |||  |  | | | |||   |  |  |  |  || | | ||   |     | |  || |||                                                                                                
AGGTCCATGGCTCCGGATTCCGTCGAATTCTGTTGTTGGCGTTGTGTATCTCCGGGATCTGGTCCGCCTACATCTACCAAGGCGTTCTTCAAGAGACTCTgtaagtaaaattgttaggtcatatcgattctcgtcgtcttcattgctcgattcagcttgttgttgcgaaatagttg--ctacagagtcattgattcgtttctattcgcaatctgtggtttgaatttctatagacatagctgccggaatttgttcttggtacatggactaatgaaattcgtttatctgattag

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|78118465|gb|DV536850.1|DV536850
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211352183|gb|FL343466.1|FL343466
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|148931883|gb|EC877348.2|EC877348
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|149005383|gb|EE039935.2|EE039935
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211432973|gb|FL347888.1|FL347888
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211053272|gb|FL359434.1|FL359434
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|148977669|gb|EE026096.2|EE026096
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|78080957|gb|DV509369.1|DV509369
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|148985614|gb|EE029715.2|EE029715
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|94480389|gb|EB709347.1|EB709347
EST:     GCAGGGATCTGGTCCGCCTACCTCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACCAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211537618|gb|FL330685.1|FL330685
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211335766|gb|FL352927.1|FL352927
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|38687895|gb|CK144926.1|CK144926
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGTGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|94479889|gb|EB708847.1|EB708847
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|50324993|gb|CO520119.1|CO520119
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|74234865|gb|DT642779.1|DT642779
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|148953372|gb|EE152866.2|EE152866
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211189091|gb|FL366154.1|FL366154
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211523327|gb|FL357648.1|FL357648
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|78107092|gb|DV525510.1|DV525510
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|211190516|gb|FL321614.1|FL321614
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|71318369|gb|DR795946.1|DR795946
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|71440454|gb|DR821504.1|DR821504
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
EST: gi|101390801|gb|EB817335.1|EB817335
EST:     GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCT                         ATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT
genomic: GCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTT

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), 49 (downstream exon)
Score: 123

TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagccccc ... ggtggttcagATCGACGAAGCGGTTCGGGCCGGATGCGCGGCGGTTCGAGCACCTCGCGTTCCTCAACTTCGCGCAGAACGTCATCTGCTTCGTCTGGTCCTTCATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGGCGGCGGGAGCATGGCGGGGCGCGTGGCCGTCCTCGCCTTCTGTGTCGCAGGGATCTGGTCCGCCTACATCTACCAGGGCGTCCTCCAGGAGACTCTgtaagcccccccccctctctaattgctgtccgaagtccgctacacaattagacaagccggggtcaatttggtgagtttgctcgccggtggttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA