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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcactcatttctcataatttcttgctgaacaaagcttaaatccaactcaaatacttggccactccaggcctccagctttaaattcatacattcaacaactcaagtgctcaatctttgttcgctggtgatcaatcttgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT

Basic information

species Zea mays
transcript GRMZM2G050268_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050268_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g36740.1 (Oryza sativa), 3'ss of exon 3
gtaagtgcactcatttctcataatttcttgctgaacaaagcttaaatccaactcaaatacttggccactccaggcctccagctttaaattcatacattcaacaactcaagtgctcaatctttgttcgctggtgatcaatcttgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT
                                                                       | |   |||    |    ||||  ||||  |   |  | |||  ||||||  |   || ||  |      ||| |||||||| |||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||  | |||||||| |||||||||||||||||||||||||
---------------------------------------------------------------------gtaagaacccacacatcctctcatggattcgtctcttgcaatgca-aatcttgctcatcttgttcttgggtgtgt-gtgcagGGAAATCTGGGGTGGGCGCTGATGCAGAAGGAGAACTACACGGAGGCGGAGGGGGCGTACCGGAGGGCGCTGCTGATCGGGCCGGACAACAACAAGATGT
















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|78113367|gb|DV531759.1|DV531759
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTA
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTA
EST: gi|76294345|gb|DV033913.1|DV033913
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|76922892|gb|DV169228.1|DV169228
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|89758318|gb|DY687540.1|DY687540
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|74234535|gb|DT642449.1|DT642449
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|71775124|gb|DR973002.1|DR973002
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|211332358|gb|FL287652.1|FL287652
EST:     GGGCCGGCA-GTTCCAGGTCACTCTCGAACAAGAAGCCAC-ANGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTA-ACAGAGGCGGAG
genomic: GGGCCG-CAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|89759856|gb|DY688538.1|DY688538
EST:     GGGGCCGCA-GTTCCAGGTCACTCTCGAACAAGAGGCCACCAGGCTCCTT                         GGCAATCTGGGATGG
genomic: GGG-CCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGG
EST: gi|50322683|gb|CO517809.1|CO517809
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|71306833|gb|DR789574.1|DR789574
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|148965097|gb|EE015913.2|EE015913
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|76010983|gb|DT938153.1|DT938153
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|93283827|gb|EB676091.1|EB676091
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|149095665|gb|EE181288.2|EE181288
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|60399662|gb|DN232472.1|DN232472
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|149084073|gb|EE173471.2|EE173471
EST:     AGGGCCGCAGGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACCGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|76292412|gb|DV031980.1|DV031980
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|211332356|gb|FL287650.1|FL287650
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAAGAGAACT
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACT
EST: gi|78104441|gb|DV522859.1|DV522859
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
EST: gi|50333368|gb|CO528494.1|CO528494
EST:     AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTT                         GGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG
genomic: AGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAG

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), 49 (downstream exon)
Score: 110

CCACCAGGGCCACGCCTTCAATGGCAAGCGGACCAAAACGGCTCGCTCTCAGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 8

CCACCAGGGCCACGCCTTCAATGGCAAGCGGACCAAAACGGCTCGCTCTCAGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 12

CCACCAGGGCCACGCCTTCAATGGCAAGCGGACCAAAACGGCTCGCTCTCAGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT


Block sizes: 32 (upstream exon), 34 (downstream exon)
Score: 3

CCACCAGGGCCACGCCTTCAATGGCAAGCGGACCAAAACGGCTCGCTCTCAGGGCCGCAAGTTCCAGGTCACTCTCGAACAAGAAGCCACCAGGCTCCTTgtaagtgcac ... tgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaacaactcaagtgctcaatctttgttcgctggtgatcaatcttgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT
                                          tcttgtt  CT-rich tract
                   aatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcactcatttctcataatttcttgctgaacaaagcttaaatccaactcaaatacttggccactccaggcctccagctttaaattcatacattcaacaactcaagtgctcaatctttgttcgctggtgatcaatcttgttgtgcagGGCAATCTGGGATGGGCGCTGATGCAGAAGGAGAACTACACAGAGGCGGAGGGGGCGTACCGTCGTGCGCTGCTCATCGGGCCGGACAACAACAAGATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG