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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtagaaatactttcctgaatgccttgtcccttgaagacgcctctcttgaagacatgctggttgttttgacttctaatcccttgtggcctaccttcaatgcag

Basic information

species Zea mays
transcript GRMZM2G409407_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409407_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G08090.1 (Glycine max), 5'ss of exon 4
CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtaga-------------aatactttcctgaatgc------------cttgtcccttgaagacgcctctcttgaagacatgctg-gttgttttgacttctaatcccttgtggcc-taccttcaatgcag
 |||||    ||| | ||| | |||||||||||||| |||||||| || || |||||||| ||| ||||| | ||||||||  | || | ||||| ||| |||    || |             | || |||  ||  |               || |    ||   |    || |||| |   | |      | ||     ||   ||   || || || ||  | |  |||||
AAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGAGGCTCAAAACCTACAAGGCTAAGTTGGTTGTGTTCCCAAGAAGGGCACACAAGGTCAAGgtaaagctaaattcttcaattattattaatttgatggttatgtgcaaattttatttattttatggtcatcattcccttggaagtaggaaacaatattgaagtttgagattgtttatgtccctatttgctttgcag

upper sequence: GRMZM2G409407_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G17370.2 (Glycine max), 5'ss of exon 3
CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtagaaatactttcctgaatgccttgtcccttgaagacgcctctcttgaagacatgctggttgtt-ttgacttctaatcccttgtggcctaccttcaatgcag--------------------------
 |||||    ||| | ||| | |||||||||||||| |||||||| || || |||||||| ||| ||||| | ||||||||  | || | ||||| ||| |||    |  |||| |||   | | |   |||    ||  |   ||   | ||    |  |  ||||  |  ||  ||| |||    |        |  ||  |    |                          
AAAGAATCGTTCTTTGGAGAGTCTGCAGGCCAATGTGCAGAGGCTCAAAACCTACAAGGCTAAGTTGGTTGTGTTCCCAAGAAGGGCACACAAGGTCAAGgtaaagct--aaattcttcaatcattaatttgatgatt--atgtgcaaattttatttattttatggtcatcattaccttgtaagtagtaaacattgaagtttgagattgtttacatccctaattttgctttgcag

upper sequence: GRMZM2G409407_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT3G48960.1 (Arabidopsis thaliana), 5'ss of exon 3
CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtagaaatactttcctgaatgccttgtcccttgaagacgcctctcttgaagacatgctggttgttttgacttctaatcccttgtggcctaccttcaatgcag
|||||||   ||| | |||||  | ||  |||| ||||||||||| || || |||||||| ||| |||||||||||||  |  |||| || | || ||| |||    |    |  |       | ||  ||     |   ||  | || | |  | |  |||    | | | |||  |||      || ||   |   ||   |  ||
CAAGAACCGGTCTTTGGAGGGTTTTCAAACCAACGTCCAGAGGCTGAAAACCTACAAGGCTAAGTTGGTTATCTTCCCGCGCTGTGCCCGAACGGTCAAGgtactccttcgcaagc------aactggtttagggttc--agtggactgtatgaatggaatggatttggatatgatctctttgttgttatgcttttgtttgtgtttag

upper sequence: GRMZM2G409407_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0047g01160.t01 (Vitis vinifera), 5'ss of exon 3
CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtagaaatactttcctgaatgccttgtcccttgaagacgcctctcttgaagacatgctggt-tgttttgacttctaatcccttgtggcctaccttcaatgcag
 ||||||   ||||| ||| | || || || |||||||||||| | ||||| |||||||||||  ||||| |||||||||| |||||||||||   ||| ||   | ||     |||   |  ||||| ||         | | ||    | |      ||| |    |  | | | | ||   |  |||  ||               
TAAGAACCGTTCTCTAGAGAGCCTTCAAGCAAATGTCCAGAGGTTGAAGACATACAAGGCCAAATTGGTTGTCTTCCCAAGACGTGCTCGCAAATTCAAGgtcatttta-----actggacgaaatgcttttgattaaacaaaagctatccatttctgtatgttaacatcatgttattgctctccttttgctgcag-------------

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|13558589|gb|BG549945.1|BG549945
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|211266082|gb|FL031061.1|FL031061
EST:     GTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGTCAAAT                         GCCGGGGACTCTACTCGGGAAGAGCTTGCCACG-CCACCCAGGGTC-AGG
genomic: GTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAA-Tgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGG-TCCAGG
EST: gi|211247720|gb|FL179850.1|FL179850
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|211456254|gb|FL273553.1|FL273553
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|211129396|gb|FL066372.1|FL066372
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|78085923|gb|DV514316.1|DV514316
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|211266087|gb|FL031066.1|FL031066
EST:     CGTACAAGGCCAAGCTGGTTATCTTCNCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCG
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCG
EST: gi|33091972|gb|CF051966.1|CF051966
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTA
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTA
EST: gi|211263650|gb|FL031054.1|FL031054
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGTCAAT                         GCCGGGGACTCTACTCCGGAGGA
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGA
EST: gi|44900414|gb|CK826959.1|CK826959
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGC
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|27522089|gb|CA989195.1|CA989195
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|32859116|gb|CD998797.1|CD998797
EST:     GTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: GTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|6973668|gb|AW438242.1|AW438242
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|29946616|gb|CB816239.1|CB816239
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|211266077|gb|FL031056.1|FL031056
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAG
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAG
EST: gi|7238188|gb|AW573410.1|AW573410
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|116829000|gb|EC863170.1|EC863170
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGCT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|78086900|gb|DV515293.1|DV515293
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|78180971|gb|DV551344.1|DV551344
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAAT                         GCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGT
EST: gi|211263645|gb|FL031049.1|FL031049
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGTCAAT                         GCCGGGGACTC
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTC
EST: gi|211266081|gb|FL031060.1|FL031060
EST:     CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGTCAAT                         GCCGGGGACTCTA
genomic: CGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTA

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: 2674

CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGTGACTACATGCCTATTACTCGTGGTGAGAAGCGCTCAGTCGAGGTTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1774

CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGTGACTACATGCCTATTACTCGTGGTGAGAAGCGCTCAGTCGAGGTTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1109

CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGTGACTACATGCCTATTACTCGTGGTGAGAAGCGCTCAGTCGAGGTTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1897

CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtag ... ttcaatgcagGCCGGCGACTCTACTCCGGAGGAGCTTGCCACGGCCACCCAGGTCCAGGGTGACTACATGCCTATTACTCGTGGTGAGAAGCGCTCAGTCGAGGTTGTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGAGGCTTAAGACGTACAAGGCCAAGCTGGTTATCTTCCCAAGGCGTGCTCGCAAGGCCAATgtatgtgtagaaatactttcctgaatgccttgtcccttgaagacgcctctcttgaagacatgctggttgttttgacttctaatcccttgtggcctaccttcaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG