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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtccttttctacatacacatgaacaaaatcataatgaactatttgtcagtactgtgtgcagcatattgaattgtgtattgtataattgtgcaaaat...

Basic information

species Zea mays
transcript GRMZM2G099452_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 6
CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcct-tttctacatacacatgaacaaaatcataatgaactatttgtcagtactgtgtgcagcatattgaattgtgtattgtataa-ttgtgcaaaat--
||||||||||||||||||||||||||||||||||||||||||||||| ||||||||    ||||||||||| |||||| || |||||||||| ||||| ||||||| || ||| | |||  |  | | |  ||  ||  ||   | | | | | |||  |||   | ||||  | |  ||      | || |||| ||||||  
CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAAAATCATTTGGTGCTAGGAAATGGGAAACTTCTTCCTGGACTTGGTGTATCACgtaagttctgtttattcatgtattttagctcaa--attttggttt-tctattactac-atgtatggtatatgcattcatgggcaacaaaaattgtacaaaatga

upper sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT4G30020.1 (Arabidopsis thaliana), 5'ss of exon 7
CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtc---cttttct---acatacacatgaaca---aaatcataatgaactatttgtcagtactgtgtgcagcatatt--gaat-tgtgtattgtataattg-tgcaaaat---------------
|| |||||||| ||||| ||||||| | ||||||| ||||||||||| |||||| | || || |||||||| ||| |  || | ||| | ||| ||||||||||||    | |||||   |  || | ||| | |   | |  ||| | |  |||||   |  |   |||  ||  ||||  || | | | |||||  |  ||| || |  ||               
CCTTGGATAACTACTGTGGCTGCTGCAATTGATGATCGCAGATACAAAAATCATCTGACTCTTGGAAATGGTAAAATGCTTGCCGGAATAGGATTATCTCgtaagtttctcctttctctgatctagatatgtagatccacacaatagtaatttatttaagaagagactgt-tagtttattctgagtctctctattggttttttgatgaatcattatgcgtttgtgcag
















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|32796667|gb|CD948903.1|CD948903
EST:     TAACACTAGGAAATGGAAAACTTATTTCTGGACATGGAGTATCTC                         CTGCAACACATGGGAATTTGTCATTTAGCCTGATTTCTGCAGCTGATGCTC
genomic: TAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|86472826|gb|DY239196.1|DY239196
EST:     TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGAATATGTCGTTTACCCTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|31355042|gb|CD439399.1|CD439399
EST:     TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|60358693|gb|DN225666.1|DN225666
EST:     TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|60358392|gb|DN225365.1|DN225365
EST:     TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|31356446|gb|CD440803.1|CD440803
EST:     TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGAATATGTCGNTTAGCCTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|31611998|gb|CD568620.1|CD568620
EST:     CACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCT
genomic: CACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACAT-GGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCT
EST: gi|19351725|gb|BM896257.1|BM896257
EST:     TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTC                         CTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
genomic: TCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTC
EST: gi|19351594|gb|BM896126.1|BM896126
EST:     TTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGTAGTATCTC                         CTGCAACACATGGTGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGC
genomic: TTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGG-AGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGG-GAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGC

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: 126

CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTCTTCTGGGCTCATCTGCAAGCAAGTACAGTGCATTAGACTGTCAGAGGCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 16

CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTCTTCTGGGCTCATCTGCAAGCAAGTACAGTGCATTAGACTGTCAGAGGCC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTCTTCTGGGCTCATCTGCAAGCAAGTACAGTGCATTAGACTGTCAGAGGCC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 43

CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtcctt ... tacaatacagCTGCAACACATGGGAATATGTCGTTTAGCCTGATTTCTGCAGCTGATGCTCTTCTGGGCTCATCTGCAAGCAAGTACAGTGCATTAGACTGTCAGAGGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGGATAACCACTGTTGCTGCTGGAGTTGATGACCGCAGATACAAGAATCATTTAACACTAGGAAATGGAAAACTTATTTCTGGACTTGGAGTATCTCgtaagtccttttctacatacacatgaacaaaatcataatgaactatttgtcagtactgtgtgcagcatattgaattgtgtattgtataattgtgcaaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaaaa