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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgtacgataggcgccgcctggaagtctggaactcagatcgggctgtcgggttttggtttcgttcgatcgatttcgctgggtgtctctctcggggtgctcaactgctcacgcgtggttaatttctcgctttggtttcag

Basic information

species Zea mays
transcript GRMZM2G157675_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157675_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 1
CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgta-cgt-acgtacgataggcgccgcctggaagtc-tggaactcagatcgggctgtcgggttttggtt--tcgttcgatcgatttcgctgggtgtctctctcggggtgctcaactgctcacgcgtggttaatttctcgctttggtttcag----------
                                    | |||| |   || | | |||||||||||||||||||| || |||||||| |||||||||||||| |  || |  | |    | | |  |||      | || |||| || ||       | ||||   | |    |||  ||  |||| | || | || | |   | | ||    |   || | |  |    || |  |    ||| ||              
------------------------------------CTGCCATCT-AGCTAGCAAAGATGATCTCCCCGGACGCGGCTCGCAACGTCGTCGGCATCATCGGCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCCGTgtaactaagctctctaaacccggttgctgctagctgtttaattaattt-gatgagggtttttggtgagatgtgaga--actgaagaattaacaaatcttgatcttgtttgtgtgtgtgtgcag

upper sequence: GRMZM2G157675_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 5'ss of exon 1
CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgta-cgt-acgtacgataggcgccgcctggaagtc-tggaactcagatcgggctgtcgggttttggtttcgttcgatcgatttcgctgggtgtctctctcggggtgctcaactgctcacgc-gtggttaatttctcgctttggtttcag----------
                                                         ||||||||||||||||| || |||||||| |||||||||||||| |  || |  | |    | | |  ||| |    | || || | || ||      ||  |        ||| |||| | || || ||  |  |        || | |   ||  |  |  | |   || |||||| | | ||  |  |           
---------------------------------------------------------ATGATCTCCCCGGACGCGGCTCGCAACGTCGTCGGCATCATCGGCAATGTCATCTCCTTCGGCCTCTTCCTCGCCCCCGTgtaattaagttcttctaatcaagccga----tcgatcgacc-atctctctctgcatgcaggataggatacaatacaacaaattctgaaattcatttctggttgtgtgtatatatgtatgcag
















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|211344463|gb|FL201420.1|FL201420
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|31628388|gb|CD526584.1|CD526584
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGNCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211162574|gb|FL132733.1|FL132733
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|28188031|gb|CB179641.1|CB179641
EST:     GGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: GGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|37361467|gb|CF602756.1|CF602756
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211342073|gb|FL201410.1|FL201410
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|31627932|gb|CD526360.1|CD526360
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|28188247|gb|CB179857.1|CB179857
EST:     GGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: GGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211344467|gb|FL201424.1|FL201424
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211342078|gb|FL201415.1|FL201415
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211342077|gb|FL201414.1|FL201414
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|37361336|gb|CF602625.1|CF602625
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211344465|gb|FL201422.1|FL201422
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211342079|gb|FL201416.1|FL201416
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTSTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|30160668|gb|CB924397.1|CB924397
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|148934526|gb|EC878568.2|EC878568
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|31628107|gb|CD526445.1|CD526445
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211342076|gb|FL201413.1|FL201413
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|14245092|gb|BG873674.1|BG873674
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211344464|gb|FL201421.1|FL201421
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211342075|gb|FL201412.1|FL201412
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGMMTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|71317142|gb|DR795259.1|DR795259
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211344466|gb|FL201423.1|FL201423
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|28187755|gb|CB179365.1|CB179365
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211344462|gb|FL201419.1|FL201419
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|28188001|gb|CB179611.1|CB179611
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|24462465|gb|BM659996.1|BM659996
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|28187611|gb|CB179221.1|CB179221
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
EST: gi|211344460|gb|FL201417.1|FL201417
EST:     ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCG                         GCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT
genomic: ACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT

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: 35 (upstream exon), 27 (downstream exon)
Score: 3

CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT


Block sizes: 32 (upstream exon), 37 (downstream exon)
Score: 4

CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 574

CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgt ... ttggtttcagGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAGCCCGGCCCGTTCCAAAACCTCCGTAGCCGCCGCCGCCACCCCGGCGACCGAAGATGATCTCCCCGGACGCAGCCCGCAACGTAGTCGGCATCATCGgtacgtacgtacgataggcgccgcctggaagtctggaactcagatcgggctgtcgggttttggtttcgttcgatcgatttcgctgggtgtctctctcggggtgctcaactgctcacgcgtggttaatttctcgctttggtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG