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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccttttgcttgagagatggttaggaggctggctatggattatgtgtctgcttcgatcgttttctcatgctaatgtgactcctgccgcacatgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGT

Basic information

species Zea mays
transcript GRMZM2G083716_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 1
tcccttttgcttgagagat--ggttaggaggctggctatggatta------tgtgtctgctt-cgatcgttttctcatgctaatgtgactcctgccgcacatgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGG-GCTAACTTCAGAGT------
   ||||    || ||  |     |  |   |    |   || ||      |  |  |||||  ||| |||    |||| ||||||      ||| | |||       |||  |||||| || || ||||||||||||||||| |||||||| |||||||| ||||| || |    |||      |||||  ||  || | ||||    |      
--actttcatgtgggacctccacctcagcttccattttctgaatagaagcttaagcatgcttatgattgttgctccatgttaatgttgtcattgctgaaca------gGAAATCATGGCTTCAACATTCGGTGCCACTTCTACGGTTGGCCTCATGGCTGCGCCAACCGGAAT---TGTA-----TCAGACAAGAAGCCATCTTCTCTATCTTCGG
















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|149009207|gb|EE041320.2|EE041320
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211425622|gb|FL361850.1|FL361850
EST:     TCTCCGCCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: -CT----CTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|6636998|gb|AW261270.1|AW261270
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211412337|gb|FL345665.1|FL345665
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211529294|gb|FL356728.1|FL356728
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|71764884|gb|DR962821.1|DR962821
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211472722|gb|FL335027.1|FL335027
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|148941096|gb|EC885959.2|EC885959
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211402127|gb|FL345609.1|FL345609
EST:     TCTCCGCCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: -CT----CTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|149080249|gb|EE169273.2|EE169273
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211322750|gb|FL352371.1|FL352371
EST:     TCTCCGCCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: -CT----CTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|148959020|gb|EE010533.2|EE010533
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211277762|gb|FL330400.1|FL330400
EST:     TCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCNCGAGTAG                         AAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCT
genomic: TCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAG--CGCG-AGgtgagtccgc ... catgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCT
EST: gi|148963973|gb|EE015101.2|EE015101
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|78080918|gb|DV509330.1|DV509330
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211003840|gb|FL306635.1|FL306635
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|148940496|gb|EC885295.2|EC885295
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211393798|gb|FL326098.1|FL326098
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAG                         AAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTG
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGgtgagtccgc ... catgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTG
EST: gi|211046076|gb|FL310634.1|FL310634
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211301789|gb|FL326006.1|FL326006
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211509889|gb|FL321846.1|FL321846
EST:     TCTCCGCCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: -CT----CTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|149099158|gb|EE185183.2|EE185183
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|149075815|gb|EE164351.2|EE164351
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|148983129|gb|EE029060.2|EE029060
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211055913|gb|FL348005.1|FL348005
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211053293|gb|FL359912.1|FL359912
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|148961770|gb|EE012547.2|EE012547
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAG                         AAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTG
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGgtgagtccgc ... catgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTG
EST: gi|211419075|gb|FL312381.1|FL312381
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211510315|gb|FL346123.1|FL346123
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|211503202|gb|FL344792.1|FL344792
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCAT-CGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|149013866|gb|EE043351.2|EE043351
EST:     CTCCGCCTCCGCCTCCCGCCGTCCCCTC-CGACCCAT-CACAAGCGCGAGTAG                       
genomic: CT----CTCCGCCTCCCGCCGTCCCC-CGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt
EST: gi|148983089|gb|EE029008.2|EE029008
EST:     TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGTAG                       
genomic: TTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGC--G-AGgtgagtccgc ... catgcagt

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 3 RNA-Seq libraries.


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 18

ATCGACACACGCAGCCGCGACCTGACCCGACCCTCCCGAGGCCGCCAGCCTTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGgtgagtccgc ... catgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 38

ATCGACACACGCAGCCGCGACCTGACCCGACCCTCCCGAGGCCGCCAGCCTTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGgtgagtccgc ... catgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGT


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 36

ATCGACACACGCAGCCGCGACCTGACCCGACCCTCCCGAGGCCGCCAGCCTTATCCTCTCCGCCTCCCGCCGTCCCCCGCGACCCATCCGCAAGCGCGAGgtgagtccgc ... catgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgcttcgatcgttttctcatgctaatgtgactcctgccgcacatgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGT
                       tgctaat  putative branch site (score: 36)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccttttgcttgagagatggttaggaggctggctatggattatgtgtctgcttcgatcgttttctcatgctaatgtgactcctgccgcacatgcagtagAAGACATGGCCTCGACGTTCGGTGCCACTTCTACAGTTGGCCTTATGGCTGCTCCAACGGGGAAGAATGTGCGCCTTCAGAGGAGGGCTAACTTCAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG