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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcgcatggatccccattctcttccgcgcatgcatgctccatccgagaccgcatctctctctctctcgatttgcttcttcagttcactggtgcc...

Basic information

species Zea mays
transcript GRMZM2G074672_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074672_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g23300.1 (Oryza sativa), 5'ss of exon 1
TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcgcatggatccccattctcttccgcgcatgcatgctccatccgagaccgcatctctctctctctcgatttgcttct-tcagttcactggtgcc-
||||||| || |||||||||||||||||| ||||||| ||||| |||||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||     |   |     | |          ||        |  |||    |  |   |||  ||||    || |  |||| |   |||  || |  | 
TCGCCGCCGGCCTGTCCGGCGCCAACGCCCCCTCCGCCCTCGTCCTCACCGCCGGCCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGCCTCGGAGGgtaagcccaaaaccaaaaataaataaaaataaaacaaaataaaactttcctcctcttc--ttcttcctctgcaaatctctttctgttttttctttgatttct

upper sequence: GRMZM2G074672_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G05230.1 (Glycine max), 5'ss of exon 1
TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcgcatggatccccattctct-tccgcgcatgcatgctccatccgagaccgcatctctctctctctcgatttgcttcttcagttcactggtgcc
|||| || || || ||||| ||||| ||| ||||| |  | || |||||||| ||  | ||||| |||||||||||||||||||||||||| ||||| ||||| | ||  ||    ||  ||  |||  | |         ||   ||   | | |   || | || || |   |                          
TCGCTGCCGGACTCTCCGGAGCCAATGCCACCTCCTCCATTGTTCTCACCGCCGGCATAGCCGAAGTCGCCGCCGGCGCCATCTCCATGGGTCTCGGCGGgtacgtttaacaaaactcttcacactcaattcaacttcttttggagcaaaaggggcta-atgtttcactgtgcag--------------------------

upper sequence: GRMZM2G074672_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G34430.1 (Glycine max), 5'ss of exon 1
TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcgcatggatccccattctcttccgcgcatgcatgctccatccgagaccgcatctctct-ctctctcgatttgcttcttcagttca-----ctggtgcc-----------
|||| || || || ||||| ||||| ||| ||||| |  | || |||||||| ||  | ||||| || ||||||||||||||||||||||| ||||| ||||| | ||  |     ||  ||  |||       | | | ||   | |  |  | |   || |  | | |     ||||  ||    ||   |     ||  ||             
TCGCTGCCGGACTCTCCGGTGCCAATGCCACCTCCTCCATTGTTCTCACCGCCGGCATAGCCGAAGTTGCCGCCGGCGCCATCTCCATGGGTCTCGGCGGgtacgtttaaccaaactcttcacactcaatttaac-tacttgagtcttgaggtatcatttcacgttgcacagaaaatttaattacggagcaaaaggggctaatgtttcactgtgcag

upper sequence: GRMZM2G074672_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0011g06000.t01 (Vitis vinifera), 5'ss of exon 1
TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcgcatggatccccattctcttccgcgcatgcatgctccatccgagaccgcatctctctctctctcgatttgcttcttc--agttcactggtgcc
| ||||||||  ||||||| ||||| ||||||||  |  || | |||||||| ||  |||| || ||||| || ||||||||||||||||| ||||| |||||   || |||         ||    ||       |  ||    | ||   ||| |  | |   |  |     |     |       |    | |   |  
TTGCCGCGGGTTTGTCCGGTGCCAATGCCTCCTCTTCTATCATTCTCACCGCCGGCATCGCAGAAGTCGCTGCTGGCGCCATCTCCATGGGACTCGGCGGgtat-ttttgcaaattatttgatgtgtttgtttagtttaatttcgcttcatggacggtgtttggttgccgagaaaaaaaatggaaagaaagaaattaaaga-

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|211529081|gb|FL234917.1|FL234917
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|148942328|gb|EC887346.2|EC887346
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|14242908|gb|BG840239.2|BG840239
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|71444738|gb|DR825788.1|DR825788
EST:     GGGGCTC-GAGGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGC
genomic: GGGGCTCGGA-GGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGC
EST: gi|71444739|gb|DR825789.1|DR825789
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211526087|gb|FL234907.1|FL234907
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211529073|gb|FL234909.1|FL234909
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211529076|gb|FL234912.1|FL234912
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211529078|gb|FL234914.1|FL234914
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|76019557|gb|DT946727.1|DT946727
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211526083|gb|FL234903.1|FL234903
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211526086|gb|FL234906.1|FL234906
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211529074|gb|FL234910.1|FL234910
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|76020433|gb|DT947603.1|DT947603
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
EST: gi|211526085|gb|FL234905.1|FL234905
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTANCA-CCGGGAGCTGCAGC
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTA-CAACCGGGAGCTGCAGC
EST: gi|211526088|gb|FL234908.1|FL234908
EST:     GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGG                         GTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG
genomic: GCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCG

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: 46 (upstream exon), 43 (downstream exon)
Score: 13

TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 14

TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 3

TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcg ... gtgcgttcagGTACCTGGCGGCGAAGAGCGAGGCTGACCACTACAACCGGGAGCTGCAGCGCGAGCAGGACGAGATCGACACCGTCCCCGACGTCG


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
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TCGCCGCGGGGCTGTCCGGCGCCAACGCCTCCTCCGCGCTCGTGCTCACCGCGGGGCTCGCCGAGGTCGCCGCCGGCGCCATCTCCATGGGGCTCGGAGGgtaagcttcgcatggatccccattctcttccgcgcatgcatgctccatccgagaccgcatctctctctctctcgatttgcttcttcagttcactggtgcc

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