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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccaccaccgtcccttcctgctctctgcacccccacccccctagcccttgctctcttcattcacatacatgcagtacatctctcctcgactagtac...

Basic information

species Zea mays
transcript GRMZM2G092468_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 5'ss of exon 2
AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccaccaccgtcccttcctgctctctgcacccccacccccctagcccttgctctcttcattcacat---acatgcagtacatctctcctcgactagtac
||||||| ||||||||||| ||||||||||||||  | ||||||||||| ||||||||| |||||||||| |||||||||||||||||||||||||| ||||    | || |  |   ||  |  | ||  || |   ||    |   |   |   |||||   | | ||   |      ||   |||    | | ||| || 
AGCTCGCCCGCTACAAGGACCAGATCAAGAAGACCAGGCCAGGCCCCGCCCAGGAGGCCATCAAGGCACGCGCCATGAGGGTCCTCAAGCAGCGCAGAATgtatatctcccc--ttttttttttatttcatcatcattacttatcatacttatatactcttagattagattagaagattggttactctacttttgcctaata-

upper sequence: GRMZM2G092468_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S54_150V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtga-gccaccaccgtcccttcctgctctctgcacccccaccccccta-gcccttgctctcttcattcacatacatgcagtacatctctcctcgactagtac
||||     | ||   |||||||||||||||||| || |||||||| || || |||||||| ||||| || |||||| |  |  | ||||||   |  |||| | | ||       | |||  || | ||    ||    |           | |  | | |||||   ||| || |   |  |       |  ||  ||| 
AGCTGTTCAGGTATCGGGAGCAGATCAAGAAGACTCGGCCAGGCCCTGCGCAAGAGGCCGTGAAGGCCCGTGCCATGCGAATTTTGAAGCAGAAGAAAATgtaaagacagtttgtcctctttttggtttccctcccgttgcgaataggtagtcgtattatgttcatg-gcatccaagagatgaacaggatttgcaccggta-
















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|37622046|gb|CF675099.1|CF675099
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|18165330|gb|BM335169.1|BM335169
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211387542|gb|FL169282.1|FL169282
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCACGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211087643|gb|FL395856.1|FL395856
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211439056|gb|FL385005.1|FL385005
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|13562177|gb|BG550397.1|BG550397
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|5928953|gb|AW056245.1|AW056245
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGNGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|87151661|gb|DY396450.1|DY396450
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|32908604|gb|CF013417.1|CF013417
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|15312803|gb|BI478393.1|BI478393
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACA
EST: gi|22489538|gb|BU049461.1|BU049461
EST:     AAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: AAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211211675|gb|FL370026.1|FL370026
EST:     CAGGAGGCCGTCAAGSSACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211387544|gb|FL169284.1|FL169284
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211406647|gb|FL439010.1|FL439010
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|17970239|gb|BM277003.1|BM277003
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|71437048|gb|DR818098.1|DR818098
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|32916309|gb|CF021121.1|CF021121
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAATATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211394823|gb|FL369347.1|FL369347
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|32863022|gb|CF002704.1|CF002704
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211439568|gb|FL408949.1|FL408949
EST:     CAGGAGGCCGTCAAGS-ACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211161696|gb|FL418714.1|FL418714
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCA
EST: gi|211408542|gb|FL414508.1|FL414508
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCN
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211348483|gb|FL394288.1|FL394288
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACC
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACC
EST: gi|76286967|gb|DV026535.1|DV026535
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211434160|gb|FL401089.1|FL401089
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
EST: gi|211387541|gb|FL169281.1|FL169281
EST:     CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGAT                         GTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA
genomic: CAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 77

AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 348

AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccacc ... ttttttacagGTACGAAGGGCAGCGTGACATGCTCTACAACCAAACATATAACCTTGACCAAGTTGCTTTTGCGGCAGAGGGACTTAAAGATGCTCAGCAAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCGCGCGCTACAAGGAGCAGATCAAGAAGACGCGCCCAGGCCCCGCTCAGGAGGCCGTCAAGGCACGAGCCATGAGGGTCCTCAAGCAGCGCAGGATgtgagccaccaccgtcccttcctgctctctgcacccccacccccctagcccttgctctcttcattcacatacatgcagtacatctctcctcgactagtac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgtccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccct