Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctccctattgacaggaataattagaattctagagtagtgttcccatccagactgactatttttgtcaaattaattttattgtactgaaattattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT

Basic information

species Zea mays
transcript GRMZM2G144387_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144387_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44450.2 (Oryza sativa), 3'ss of exon 1
----ttctccctattgacagg--aataattagaattctagagtagtgttcccatccagactgactatttttgtcaaattaattttattgtactgaaattattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT
    || |  ||    | |||  | | ||  | ||   | |     ||||   |     ||||  |   ||  |    | |  ||   ||  | ||    ||||||||||||||||   |||  | ||||||| |||||||||||| ||||||||||  |||||||||||   ||||||||||| ||||| || || |||||||||
tagattatgtctgaatataggttactgatcggtataagaaatgctcgttctt-tgtttcctgaacaaaattcacgtgctgagcttgc-gtgatcaa----ttgcagTAAGTTGCAGAGCGAGGTTCTCAAGGAAGCCATCTCCCAGGTTGTTGGGGAATCCAAGGAGAAGGGCAGGAAGTTCACCGAGACCGTTGAGCTTCAGATT

upper sequence: GRMZM2G144387_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44380.2 (Oryza sativa), 3'ss of exon 2
ttctccctattgacaggaataattagaattctagagtagtgttcccatccagactgactatttttgtcaaatt---aattttattgtactgaaattattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT
   |   |  |  |||       |  | |  | ||  ||| |    |       |   | |   |  ||||||   ||| | |   |     |   ||||||||||||| ||  | ||| || ||||||| |||||||||||| ||||||  |||  |||||| ||||| ||||||||||| ||||| || || ||||| |||
---tagattataccagagtatggtgcactgattgatgagtatcagaaatgttctttcttttccataacaaattctgaatgtgagcttgtgcgatcaattgcagTAAGTTACAAACCGAGGCTCTCAAGGAAGCCATCTCCCAGGTTGTTGCTGATTGCAAGGAAAAGAACAGGAAGTTCACCGAGACCGTTGAGCTTCAAATT

upper sequence: GRMZM2G144387_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 3'ss of exon 1
ttctccctattgacaggaataattagaattctagagtagtgttcccatccagactgactatttttgt-caaattaattttattgtactgaaatta-ttgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT
   |    | |   |||  |  |   |    | || | ||     || ||     | | | ||        |    |  | || | |||   |    ||||||||| | |||   ||     ||| ||| |||||| | ||||||      |  || ||||||||||||||||||||||| ||||||||||| |||||||| 
--atggggagttttagggtttttagtagggtttgattggtagctacaacctactagtcgaattacacgtttaacggtcgtgttatgctgctctcggctgcagTAAGCTTCAGAGCGATGTCCTCAGGGAGGCCATCACTCAGATTACCACTGCCGCTAAGGAGAAGAATAGGAAGTTCACAGAGACTGTGGAGCTTCAGATC

upper sequence: GRMZM2G144387_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 3'ss of exon 1
ttctccctattgacaggaataattagaattctagagtagtgttcccatccagactgactatttttgtcaaattaattttattgtactgaaattattg----cagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT
   |   |  ||    | | ||||    | ||   ||    |    |       | |   ||  | |  |  | |      || | |||  || | |    ||||||| | |||   ||     ||  ||| |||||  | |||||       |  ||||||||||||||  ||||||||||||| ||||| || |||||||||
---tgagttctgctttgga-aatttagttcctgtggtgagttgtttaatggttgttaggtttaatttgtagctgacggacgtggaatgattttttcggacgcagTAAGCTCCAGAGCGATGTCCTCCGGGAGGCCATTACGCAGATCACCACTGCGGCCAAGGAGAAGAACCGGAAGTTCACTGAAACTGTAGAGCTTCAGATT

upper sequence: GRMZM2G144387_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 3'ss of exon 1
ttctccctattgacaggaataattagaattctagagtagtgttcccatccagactgactatttttgtcaaattaatttta--ttgtactgaaattatt----gcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT
      |   | ||| |||||   |   ||  | | |||  || | |  | |    ||| ||||  | | ||  |  | |  | |   | ||  ||||     ||||||| | |||  |||   | | | ||| || ||| | ||||| || |  |  |||||||||||||||||||||||||| |||||||| ||||||||||| 
----gtcaggtaacacgaatatgaaatcttggaaattaggtttacgactctggt--actgttttgatgatatggaactgaaatagagtttaatgtattctcaacagTAAGCTTCAGAGTGATGTTCTGAGGGAGGCGATCACTCAGATCGTGGCTGCAGCCAAGGAGAAGAATAGGAAGTTCACAGAGACTGTTGAACTTCAGATC

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|71319472|gb|DR796481.1|DR796481
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32865991|gb|CF005673.1|CF005673
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211038053|gb|FL324592.1|FL324592
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211205849|gb|FL344234.1|FL344234
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|67031999|gb|CO460748.1|CO460748
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32831798|gb|CD971476.1|CD971476
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31361118|gb|CD445475.1|CD445475
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211128559|gb|FL314413.1|FL314413
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211396420|gb|FL326112.1|FL326112
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211522801|gb|FL337769.1|FL337769
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31558473|gb|CD527685.1|CD527685
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211333248|gb|FL338545.1|FL338545
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211267379|gb|FL327854.1|FL327854
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31356278|gb|CD440635.1|CD440635
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60346809|gb|DN213782.1|DN213782
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32915327|gb|CF020139.1|CF020139
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|5525264|gb|AI861103.1|AI861103
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32846056|gb|CD985737.1|CD985737
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211082981|gb|FL307157.1|FL307157
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71318356|gb|DR795940.1|DR795940
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211093806|gb|FL338260.1|FL338260
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211233023|gb|FL341135.1|FL341135
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31997784|gb|CD661769.1|CD661769
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71764450|gb|DR962387.1|DR962387
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211073651|gb|FL383785.1|FL383785
EST:     TCAAACCCTAAGCAGCCATGAG
genomic: TCAAACCCTAAGCAGCCATGAG
EST: gi|60356469|gb|DN223442.1|DN223442
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60349659|gb|DN216632.1|DN216632
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|67016451|gb|CO445200.1|CO445200
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|19770531|gb|BQ035252.1|BQ035252
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211316044|gb|FL324354.1|FL324354
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|12046107|gb|BF728246.1|BF728246
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71429061|gb|DR810111.1|DR810111
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211208161|gb|FL329110.1|FL329110
EST:     GCAGSCATGAG
genomic: GCAGCCATGAG
EST: gi|211314307|gb|FL338888.1|FL338888
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31359377|gb|CD443734.1|CD443734
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71439364|gb|DR820414.1|DR820414
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211193066|gb|FL327267.1|FL327267
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211346721|gb|FL310895.1|FL310895
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|18660469|gb|BM500878.1|BM500878
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|93015413|gb|EB640933.1|EB640933
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211028398|gb|FL329799.1|FL329799
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32907236|gb|CF012049.1|CF012049
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|37399690|gb|CF637178.1|CF637178
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211072619|gb|FL332510.1|FL332510
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71311310|gb|DR791971.1|DR791971
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|28361697|gb|CB240053.1|CB240053
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32907369|gb|CF012182.1|CF012182
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211510097|gb|FL332413.1|FL332413
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|116815184|gb|EC857838.1|EC857838
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|78180918|gb|DV551291.1|DV551291
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211019242|gb|FL365616.1|FL365616
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211283162|gb|FL328201.1|FL328201
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32857712|gb|CD997393.1|CD997393
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211442768|gb|FL349584.1|FL349584
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211061868|gb|FL348033.1|FL348033
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60356727|gb|DN223700.1|DN223700
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211393799|gb|FL326099.1|FL326099
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|22819612|gb|BU499702.1|BU499702
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32915734|gb|CF020546.1|CF020546
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32865077|gb|CF004759.1|CF004759
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|29130620|gb|CB381324.1|CB381324
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211289779|gb|FL366226.1|FL366226
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60395702|gb|DN228572.1|DN228572
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71437006|gb|DR818056.1|DR818056
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32863499|gb|CF003181.1|CF003181
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32862720|gb|CF002402.1|CF002402
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|93015208|gb|EB640728.1|EB640728
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|9743022|gb|BE519170.1|BE519170
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60352287|gb|DN219260.1|DN219260
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31356277|gb|CD440634.1|CD440634
EST:     GCAGACATGAG
genomic: GCAGCCATGAG
EST: gi|15053222|gb|BI358767.1|BI358767
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|29543541|gb|CB603923.1|CB603923
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32847345|gb|CD987026.1|CD987026
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60352018|gb|DN218991.1|DN218991
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|31998254|gb|CD661995.1|CD661995
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|28931172|gb|CB334533.1|CB334533
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|26557762|gb|CA829997.1|CA829997
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60354025|gb|DN220998.1|DN220998
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|71772977|gb|DR970898.1|DR970898
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|4886001|gb|AI677121.1|AI677121
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|28576041|gb|CB281933.1|CB281933
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|213170184|gb|FM193649.1|FM193649
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211185496|gb|FL313586.1|FL313586
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60345082|gb|DN212055.1|DN212055
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60349298|gb|DN216271.1|DN216271
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|120480250|gb|EH210783.1|EH210783
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211448765|gb|FL325249.1|FL325249
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211157135|gb|FL327686.1|FL327686
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211270490|gb|FL356086.1|FL356086
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211531513|gb|FL328884.1|FL328884
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|67040517|gb|CO466772.1|CO466772
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|22521050|gb|BU079861.1|BU079861
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|9733727|gb|BE512479.1|BE512479
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211510060|gb|FL330172.1|FL330172
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60352016|gb|DN218989.1|DN218989
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60352607|gb|DN219580.1|DN219580
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|84980830|gb|DW531179.1|DW531179
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211388158|gb|FL311852.1|FL311852
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|32921553|gb|CF026365.1|CF026365
EST:     GCAGTCATGAG
genomic: GCAGCCATGAG
EST: gi|71445136|gb|DR826186.1|DR826186
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|211514843|gb|FL332902.1|FL332902
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|67030302|gb|CO459051.1|CO459051
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|84980654|gb|DW531003.1|DW531003
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|60354739|gb|DN221712.1|DN221712
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG
EST: gi|9794588|gb|BE552896.1|BE552896
EST:     GCAGCCATGAG
genomic: GCAGCCATGAG

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: 40 (upstream exon), 49 (downstream exon)
Score: 18795

CCATGAGgtactctttc ... attattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 16432

CCATGAGgtactctttc ... attattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 13697

CCATGAGgtactctttc ... attattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 9620

CCATGAGgtactctttc ... attattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catccagactgactatttttgtcaaattaattttattgtactgaaattattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT
             tatttttgtcaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctccctattgacaggaataattagaattctagagtagtgttcccatccagactgactatttttgtcaaattaattttattgtactgaaattattgcagTAAGTTGCAGTCTGAGTCTGTCAAGGATGCCATCTCCCAGATTGTTGGGGATGCCAAGGAGAAGAATAGGAAGTTCACTGAGACTGTGGAACTTCAGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtactg