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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttcatttgcaaacttttttgccttagcactgtaccaggcagtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG

Basic information

species Zea mays
transcript GRMZM2G092112_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g44200.2 (Oryza sativa), 3'ss of exon 9
gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttcatttgcaaacttttttgccttagcactgtaccaggcagtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG
                                                                         |   |  || | |||     |||  |||| | | || ||   |||| |  || ||     |||| || |  || || |     | ||||||| |   ||||||| ||||||||||| ||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| |||||| ||||||| |||||||| |||||  | ||||||
-------------------------------------------------------------------------tggaaaattcactctgggggtttactttgtatatttatt---cttatc-ttgcac-----agtggaattacattatacc----aagttaataggctgcactgttaatgttcagGTTCGGTCCTGTGAATTTATTCTGGAGTACCCGATTTGACAAAGCCATGACATGGTTTCTGACTTGCTTGCAAGAATTTGCTGATTTTGCTGTTAGTTTG

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 3'ss of exon 8
gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttc--atttgcaaacttttttgccttagcactgtaccaggcagtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG
                                                                                     |||||| ||  |  |||| |  ||  ||| ||  | |   || |     || |     ||   | |   | |     |      | |   || | |    ||||||||||||||||||||| ||||||||||| || |||||||||||||||||||||||||| || ||||||||||| ||||||||||| || || || |||
-----------------------------------------------------------------------------------tttctatatttgccctatttactgacagttt-gctctgggtgtgcatttttca-tatttgttgtccctttgttgagcactgcagttatatcatgctaac---cagGTTTGGTCCCGTGAATTTATTCTGGAGCACACGTTTTGACAAAGCCATGACATGGTTTCTAACCTGCCTGCAAGATTTTGCTGAGTTCGCTATTAGCTTG

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 8
gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttcatttgcaaacttttttgccttagcactgtaccaggcagtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG
                                                                         |  || ||||     | |||  |   |   ||||||  |    ||||   ||| |          |||||    |    || |    || |||   |   | | | | |||||||||||||| || || ||||||||||| || || | ||||||||| ||||||| |||| |  | |||||  | || ||||| || ||||||| |     |
-------------------------------------------------------------------------tactaagttgtaaacaaaataat--ataataaacttcctgcttttagatttgttctta-------aacttgtcta---ctgagtcactattaatggatgttat-ggttttcagGTTTGGTCCAGTCAACTTGTTCTGGAGTACTCGCTATGACAAAGCAATGACATTGTTTTTAGCATGCCTCAAGGATTTTGCAGACTTTGCCAAATCCAAG

upper sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv15s0046g00950.t01 (Vitis vinifera), 3'ss of exon 8
gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttcatttgcaaacttttttgccttagcactgtaccaggc--agtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG
                                                                                        |||  |   |  | ||   |||  ||  |  |   || | | |||  | ||   |  ||| ||   | |||| ||  | |   |  |   |  |  | ||||||||||| ||||| ||||| |||||||| || | ||||||||| ||||| |  ||  | || |||||  | || |||||||| |||||||       |
---------------------------------------------------------------------------------------gatacatggaaagtccatggtttgatgtttaggtcatgcatctggctcattgttccccaattatatattggatcttt-tgattgattcaagtatttcttagGTTTGGTCCTGTGAACTTGTTTTGGAGCACACGCTATGACAAAGCAATGACGTTATTCTTGACATGCCTTAAGGACTTTGCTGATTTTGCCAATTCCAAG

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|32914777|gb|CF019589.1|CF019589
EST:     GTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: GTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|50327434|gb|CO522560.1|CO522560
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|71764422|gb|DR962359.1|DR962359
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|86471374|gb|DY237744.1|DY237744
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         CTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|74242756|gb|DT650670.1|DT650670
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|29545091|gb|CB605269.1|CB605269
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|67014170|gb|CO442919.1|CO442919
EST:     TGGGAAGCTTTCCCAGAGTCACAGACATCCAGAANTA-CACATATGAACT                         GGTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAACCC-TGAC
genomic: TGGGAAGCTATCCAAGAGTCACAGACATCCAGAA-TAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|7238063|gb|AW573435.1|AW573435
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACC
EST: gi|24767878|gb|CA403013.1|CA403013
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|40303501|gb|CK347888.1|CK347888
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
EST: gi|211504091|gb|FL041160.1|FL041160
EST:     ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACT                         GTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC
genomic: ATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGAC

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: 45 (upstream exon), 49 (downstream exon)
Score: 192

ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 189

ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCAGAATAACACATATGAACTgtaagctttc ... tgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG
                         atgttaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctttctgcaagcaaatgtacttctatttctctctgagatgatggtctatagtttagtagtcctcactttcttaggttgagtctataattttcatttgcaaacttttttgccttagcactgtaccaggcagtgcaacttaatcatgcttgggatgttaataagacacactgttgatgttcagGTTTGGTCCCGTGAATTTGTTCTGGAGCACCCGATTTGACAAAGCCATGACATGGTTTCTTACTTGCCTGCAAGAGTTTGCTGAGTTTGCCATAAGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA