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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGCGGCGACCAAGGCGAGGCGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgtgcgcatgagctcaagatccgctcgatttgtggaggctctgggcttggctgccccgatgccccccccccccccccccccccctgaagtggt...

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 1
GGCCGCGGCGACCAAGGCGA-GGCGCCGCAGCCGCAGCCGC---TGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgtgcgcatgagctcaagatccgctcgatttgtggaggctctgggcttggctgccccgatgccccccccccccccccccccccctgaagtggt-----------
    | ||||  |  | ||  ||||| ||||  ||| |||    |||||||||||||||| |||||||||||||| || || || || || ||||| ||||||||||||    |||       ||    | || ||||       |||||   |  | | ||  ||||    || ||| || || |     |   |  | | ||           
----GGGGCGGGCTCGTCGTCGGCGCAGCAGGGGCATCCGACGATGGAGTGGCGGTTCGCGCAGGTCTTCGGCGAGCGCGCGGCCGGGGAGGACGTGCAGGAAGgtacgt---tgc-------cttgccaccccctcgcccgcgagaggcctggcccgttgcc-ccccaccccctcccgccgcctcgagatctggtcgattcgtgcggggttgtg
















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|19057502|gb|BM736169.1|BM736169
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211386652|gb|FL015625.1|FL015625
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|149084056|gb|EE173454.2|EE173454
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|19822590|gb|BQ048614.1|BQ048614
EST:     TTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGGCAAATCTGGTGACCATCTTGCCA
genomic: TTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGAC-GTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|4753303|gb|AI657208.1|AI657208
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|148932282|gb|EC875841.2|EC875841
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|71419454|gb|DR804774.1|DR804774
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|149051574|gb|EE155673.2|EE155673
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211384020|gb|FL015615.1|FL015615
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGTGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|149108639|gb|EE292883.2|EE292883
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211386656|gb|FL015629.1|FL015629
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|78112474|gb|DV530868.1|DV530868
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|19057676|gb|BM736343.1|BM736343
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|19436843|gb|BM953253.1|BM953253
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211384023|gb|FL015618.1|FL015618
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|148945029|gb|EC890213.2|EC890213
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211386650|gb|FL015623.1|FL015623
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211384019|gb|FL015614.1|FL015614
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|9732635|gb|BE511387.1|BE511387
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATTTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|148953679|gb|EC899040.2|EC899040
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATTTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|50332602|gb|CO527728.1|CO527728
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211386648|gb|FL015621.1|FL015621
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|149076328|gb|EE164942.2|EE164942
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211386655|gb|FL015628.1|FL015628
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
EST: gi|211384022|gb|FL015617.1|FL015617
EST:     GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAG                         TTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA
genomic: GTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCA

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: 90

GGCCGCGGCGACCAAGGCGAGGCGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 75

GGCCGCGGCGACCAAGGCGAGGCGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 131

GGCCGCGGCGACCAAGGCGAGGCGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 75

GGCCGCGGCGACCAAGGCGAGGCGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgt ... ttgttttcagTTGACATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCGCGGCGACCAAGGCGAGGCGCCGCAGCCGCAGCCGCTGGAGTGGCGGTTCGCTCAGGTCTTCGGCGAACGTGCCGCGGGCGAAGACGTCCAGGAAGgtacgcacgtgcgcatgagctcaagatccgctcgatttgtggaggctctgggcttggctgccccgatgccccccccccccccccccccccctgaagtggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA