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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggcatcccccaatttgactttgcccacttattacgatgtacgcgctccgtcgttttcgttgacatgtagaatgatcgatacttgggtgtgcggtttcag

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 5'ss of exon 2
GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggcatcccccaatt-tgactttgcccacttattacgatgt---acgcgctccgtcgttttcgttgacatgtagaatgatcgatacttgggtgtgcggt-ttcag--------------------------------
||||| ||  ||||||||| |||| |||| |||||||||||| |  | |||||||||||||||||||| ||||| ||||| || ||||||||||  |||||||  |             || |  ||||   |  || |||  || |   |     ||| | | |   |   || |    |   ||    | |||     | | | || |                                 
GCCGACGACCTCCACTCCAACGGCTTCGACGACGCGCTCCTCGCTGATCTCTGCGCCGCCAAGTCCGCCGGCTCGCCCCTATCTTCCCTGCTCGCTCGAGgtatccccattctatttcgttattccttttttctttttttagaatattccatagcttccttgggtaatgaatactttgtcatgaatttgcatttgtacacgtgatatttaaagtaatggatggttggattgtgcaattttcag

upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 5'ss of exon 2
GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc---atcccccaatttgactttgcccacttattacgatgt-----acgcgctccgtcg----ttttcgtt---------gacatgtagaatgatcgatacttgggt-gtgcggttt-cag
||||| ||  ||||||||| |||| |||| |||||||||||| |  | |||||||||||||||||||| ||||| ||| | || || ||||||   |||||||  |       ||  |   |||    |||   |  || |     | |      |   ||  |||     ||| | ||         |||||||| | | || |||  |||| | ||||  ||| |||
GCCGACGACCTCCACTCCAACGGCTTCGACGACGCGCTCCTCGCTGATCTCTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccattctatttcgttattccttttttttcttttttagaattctccatagcttactttgtcatgaatttgcatttgtacacgtgacatgtaaagtaatggatggttggattgtgcaattttcag
















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|211499920|gb|FL302706.1|FL302706
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGACCCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211499915|gb|FL302701.1|FL302701
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCT
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCT
EST: gi|91876333|gb|EB406290.1|EB406290
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|148966783|gb|EE017871.2|EE017871
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211066379|gb|FL302724.1|FL302724
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211499921|gb|FL302707.1|FL302707
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAG
EST: gi|148952245|gb|EC898050.2|EC898050
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|78080728|gb|DV509140.1|DV509140
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|148966141|gb|EE017084.2|EE017084
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211499917|gb|FL302703.1|FL302703
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211066374|gb|FL302719.1|FL302719
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|101393900|gb|EB818883.1|EB818883
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|148944776|gb|EC889918.2|EC889918
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211499922|gb|FL302708.1|FL302708
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACC-TGAGGCTAGGGGCAAAGTCATAGAC
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGAC
EST: gi|211499916|gb|FL302702.1|FL302702
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAA                         GGCACTGTCAGCTGTTCAAGA
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGA
EST: gi|31361610|gb|CD445967.1|CD445967
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|71314894|gb|DR794068.1|DR794068
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|71448119|gb|DR829169.1|DR829169
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|148938292|gb|EC882596.2|EC882596
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211499914|gb|FL302700.1|FL302700
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACC-TGAGGCTAGGGGCAA
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAA
EST: gi|71770930|gb|DR968867.1|DR968867
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|14191192|gb|BG833422.1|BG833422
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGCTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|148936622|gb|EC880746.2|EC880746
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|148950925|gb|EC896556.2|EC896556
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGAC
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGAC
EST: gi|93016572|gb|EB642092.1|EB642092
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|94477192|gb|EB706150.1|EB706150
EST:     CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
genomic: CTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACG
EST: gi|211499923|gb|FL302709.1|FL302709
EST:     TGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCCGAG                         GGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGAC
genomic: TGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCC-GAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGAC

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: 47 (upstream exon), 49 (downstream exon)
Score: 32

GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 69

GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 60

GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc ... gcggtttcagGGCACTGTCAGCTGTTCAAGAACCCTGAGGCTAGGGGCAAAGTCATAGACGCCGCTACCACACTCGGAAGAACAACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggcatcccccaatttgactttgcccacttattacgatgtacgcgctccgtcgttttcgttgacatgtagaatgatcgatacttgggtgtgcggtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC