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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactgtccaattccaaatcaattcctttttccatgtccattgcaattttgaagtgtgctcatgtgctgaagcaatccatcctgtag

Basic information

species Zea mays
transcript GRMZM2G162145_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162145_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g50770.2 (Oryza sativa), 5'ss of exon 9
TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactgtccaattccaaatcaattcctttttccatgtccattgcaattttgaagtgtgctcatgtgctgaagcaatccatcctgtag-----------
||| || ||||| |||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||     ||   |  |||| |||  |     ||| |  ||   ||| |  | |||||||||| || |     ||   | |     | |            
TGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTTCCTGGTGGCAAGgtaa-----gtttcaagccaagtcatctttgccttctacttca--tgctacctagaagtgtgctaatatatgtgagtttttctgttaggattacatgtgcag

upper sequence: GRMZM2G162145_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g50770.1 (Oryza sativa), 5'ss of exon 9
TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactgtccaattccaaatcaattcctttttccatgtccattgcaattttgaagtgtgctcatgtgctgaagcaatccatcctgtag
||| || ||||| |||||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||     ||   |  |||| |||  |     ||| |  ||   ||| |  | |||||||||| || |     ||   | |     |   
TGCTACGAACCCTAATATAAGAACTTCAATGGGCTCTGCTGCATATGCACCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTTCCTGGTGGCAAGgtaa-----gtttcaagccaagtcatctttgccttctacttca--tgctacctagaagtgtgctaatatatgtgagtttttctgttag---

upper sequence: GRMZM2G162145_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv00s0225g00220.t01 (Vitis vinifera), 5'ss of exon 9
TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactgtccaattccaaatcaattcctttttccat-----gtccattgcaattttgaagtgt---gctcatgtgctgaagcaatccatcctgtag-----------------------------------------------------
||| || || ||||||||  |||| |||||||| |||||||||||||| |||||||  |||||| |  |||||||  |||| || || ||||||||||||||| | |  ||     |  ||||   ||| | |  ||||     ||| | ||  |||||   ||     |||  ||   |  |   || |||  | | |                                                     
TGCTACCAATCCAAATATTCGAACATCAATGGGATCTGCTGCATATGCACCTGAGAATGATGCATTACTCTGGAAGATAAAGTCTTTTCCTGGTGGCAAGgta-taa--gttagtgtttaaattgcttcttctgcccataaattgtctaatgttatttttctgttgatagctattgattttgaaggattcattatcttgttttctgtgcaattgacttagtttttaattttttggaaattcaaatcttttag

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|211519180|gb|FL429073.1|FL429073
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCMAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|6227156|gb|AW155685.1|AW155685
EST:     CAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAAGCGGAAGA
genomic: CAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAAC-AGCGGAAGA
EST: gi|76911457|gb|DV164279.1|DV164279
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|149069969|gb|EE158369.2|EE158369
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|78022652|gb|DV491039.1|DV491039
EST:     GTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: GTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|37379000|gb|CF626224.1|CF626224
EST:     TCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: TCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|37377656|gb|CF625451.1|CF625451
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|61119456|gb|DN560417.1|DN560417
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|60400257|gb|DN233064.1|DN233064
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|211047870|gb|FL378907.1|FL378907
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCMAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|74246062|gb|DT653976.1|DT653976
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|211354931|gb|FL467208.1|FL467208
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|40334242|gb|CK368312.1|CK368312
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|60396406|gb|DN229275.1|DN229275
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|71327501|gb|DR800359.1|DR800359
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|37378856|gb|CF626144.1|CF626144
EST:     AAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: AAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|60341542|gb|DN208515.1|DN208515
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
EST: gi|211354932|gb|FL467209.1|FL467209
EST:     CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAG                         GAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA
genomic: CTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAA

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), 46 (downstream exon)
Score: 62

TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCACCAATACGAGTGAAATTTGAGATACCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 123

TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCACCAATACGAGTGAAATTTGAGATACCAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 64

TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCACCAATACGAGTGAAATTTGAGATACCAT


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 117

TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactg ... catcctgtagGAATACATGTGCAGAGCAGAATTTAGTCTTCCTAGCATAACAGCGGAAGAAGGGGCCCCAGAAAAGAAGGCACCAATACGAGTGAAATTTGAGATACCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCACAAACCCAAATATAAGAACTTCAATGGGTTCTGCTGCATATGCTCCTGAGAGAGATGCAATGGTCTGGAAAGTAAAATCATTCCCTGGTGGCAAGgtaattactgtccaattccaaatcaattcctttttccatgtccattgcaattttgaagtgtgctcatgtgctgaagcaatccatcctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG