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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 5
ctgggccttgtcatga--agattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagctta---cattttattattttg----tttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
       ||   || |  || |  |  |    || |   | ||  |     |||||    |||  || |  ||| ||||   || ||||||  | |     ||| |||||||| |||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
------tttagaataacaaggtgttcagactaatataacttatgcattaaacatttc---tcacgggctattaaacttatgccactttattggtataacacttttgcagCTGGTATTGTCATTGAGGAGAAAAACTGGCCTCCATTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 5
ctgggc-cttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
 ||||  ||| |||        | |  | |  | |  || | | ||     |||||   || |   ||  |   | |   | | ||||  || | |  ||||||| |||||  |||||||||| |||||||| || ||| | ||| | ||||||||||||||| | ||||| || || | ||| ||||||||| |||| ||
ttgggtgcttatcaaagtttgaactcatgctttttgcttga-acaataaatatttttggtctgcttttattcttcatgtgtgtaattacattatcttacagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCATTTTTCCCAATTATCCATCATGATATCGCTAATGAAATTCCAATTCATCTTCAAAGATTGCAGTA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagct--tacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
 ||    |  |   |||   |||   |  | ||   ||| |||  | || |||||  ||| |   | |     ||  ||  | ||   ||||||||| |||||||| |||||  |||||||||| |||||||| |||||| | ||| | ||||||||||| ||  | ||||| || || | ||| ||||||| | |||||||
atgatagtactgccgaaatctatagatgtcttggaatta-tatgca-ctaattttagttctgctttggtacttctagtaggtatttacattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 5
ctgggccttgtcatgaagatt--atttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
  ||  ||| |||  ||| ||  | |  | |  | |  || |   | |  |  ||||   ||     ||  |   |     | | ||||  || |||  ||||||| |||||  |||||||||| |||||||| || ||| | ||| | ||||||||||||||  | ||||| ||||| | ||| ||||||||| |||| ||
--ggtgcttatcaaaaagtttgaactcatgctttttgcttgaacaataaatattttttggtctacttttattcttcaagtgtgtaattacattattttacagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCATTTTTCCCAATTATCCATCATGATATTGCTAATGAAATACCAATTCATCTTCAAAGATTGCAGTA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 3
ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
         ||  |     || ||     | | |   |||   ||      |  ||  |   || ||| |  | ||||| |||    |||  ||| |||||||| ||||| || ||||||||||||||||| ||||||   ||  |||| ||||| || ||  | ||||| ||||| |  || ||||||  ||| || ||
---------gtattttgagttcttcaacac-tttacataacccaacaggagtaatgccttt-agtttggtg-gtttacactttt---tttgtttttgcagCTGGAATTGTTATAGAGGAGAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 5
ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaa-gcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
          | ||| |  |  |   || | |         | | | | ||||   |||   | |    | | | ||  | |||  || |||||||  ||||||| |||||  ||||||||||||||||||| || ||  | ||| | ||||||||||||||  | ||||| ||||||| ||| || ||||   |||| ||
-ctaataacattatggacttattcaatttcctcaaacctccaaacaccccattagtttttccatgcaatttacgtttcaagttttctactttgttttccagCTGGAATTGTTCTTGAGGAGAAAAATTGGCCACCATTCTTCCCAATTATCCATCATGATATTGCGAATGAAATACCGATTCATCTACAAAAGTTGCAGTA

upper sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
       ||||| ||  | |||| |  |   ||  |  | ||    |   | | | ||   |  ||    || || | || | |||  ||| |||||||||||| |||||||| ||||||||||||||||| || ||| | || || || |||||||| ||  | ||||| ||||| |  || |  || |   |||| ||
-----gtttgtc-tgttgtttatatcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatct-aaatatcatt-ctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

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|76929603|gb|DV172080.1|DV172080
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|88755248|gb|DY539389.1|DY539389
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|211171878|gb|FL095747.1|FL095747
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCT
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCT
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCCAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|37621887|gb|CF674940.1|CF674940
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|211170205|gb|FL095740.1|FL095740
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAA
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAA
EST: gi|28566548|gb|CB278196.1|CB278196
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCCTCCTTTTCTGCCACTCATT
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCC-TCCTTTTCTGCCACTCATC
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|211171877|gb|FL095746.1|FL095746
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|38568932|gb|CF974817.1|CF974817
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|211171876|gb|FL095745.1|FL095745
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATTC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCC

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: 46 (upstream exon), 40 (downstream exon)
Score: 56

GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 95

GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 105

GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 113

GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGgtaaatactc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
                          agcttac  putative branch site (score: 113)
                                          ttttgttt  putative PPT
                             ttacattttattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgggccttgtcatgaagattatttgttccatgtttttaatataaagctcattttgtttcagaggttgctaagcttacattttattattttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - tgtcatg
- - - - - - - - - - - - - - -catgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacattt