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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatgatatataagccttcagttattctcatactagatctaaatgtttttctttttttccag

Basic information

species Zea mays
transcript GRMZM2G136769_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136769_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g39620.1 (Oryza sativa), 5'ss of exon 4
CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatgatata---taagccttcagttattctcatactagatctaaatg---tttttctttttttccag
||||||| |||||||||| |||||||||||| ||||| |||||||||| || ||||||||||||||| |||||||||| ||||| || || ||| ||||||||   |||| ||     || |  |   | ||    ||| ||  ||||| ||    |||  |||||||  |||
CCCAAATACACGCAACCTCATGGAATCAAACACTCAGTTGAGGGAAATGTTCCAAAATCCAGAATTTATTCGCCAGCTTACATCCCCAGAAACTATGCAGgtaacatatgttacgttttatgtatgtggctagctccat-ctctatctagattaactttcccttttttggcag

upper sequence: GRMZM2G136769_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0210g00220.t01 (Vitis vinifera), 5'ss of exon 4
-CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgt----tatgatatataagccttcagttattctcatactagatctaaatgtttttctttttttccag------------------------------
 ||| | |   || | | |  | || || || |||||  | || |||||  | |||||||||||||||||||| ||| |||| || || |||||  |||||||||||    || ||     | ||  || |  |     |||| | |   |  || || ||| | ||||                                 
TCCCCAGT-TGCGTAGCGTTCTTGATTCCAATCCTCAACTAAGAGAAATGATGCAAAATCCAGAATTTCTTCGTCAGTTGACTTCACCAGAGACAATGCAGgtatgtagtttaagactctgaggctctctgaaacagaaatac-atacagagttgcttctctctctttctctctcttcctcccctgccatccaggtgcatgt
















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|31356688|gb|CD441045.1|CD441045
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|32840091|gb|CD979772.1|CD979772
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|33091713|gb|CF051707.1|CF051707
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|31353322|gb|CD437679.1|CD437679
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|31350418|gb|CD434775.1|CD434775
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGCCACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|32840089|gb|CD979770.1|CD979770
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCGA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|71299524|gb|DR785772.1|DR785772
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|111990499|gb|EE331933.1|EE331933
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|32840090|gb|CD979771.1|CD979771
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|31354525|gb|CD438882.1|CD438882
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|24765744|gb|CA400903.1|CA400903
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|67040170|gb|CO466425.1|CO466425
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|67035271|gb|CO463804.1|CO463804
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
EST: gi|24768442|gb|CA403571.1|CA403571
EST:     TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAG                         CAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA
genomic: TTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAA

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: 115

CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAACCTAACCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 182

CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAACCTAACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 213

CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAACCTAACCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 144

CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatg ... ttttttccagCAATTACTCTTATTTCAGCAGTCTTTATTAGGACAGCTTGGTCAACATCAACCTAACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAAATGCACGCAACCTGATGGAATCAAACCCTCAGATGAGGGAAATATTTCAAAATCCAGAATTTCTTCGCCAGCTGACATCGCCTGAGACTTTGCAGgtatgttatgatatataagccttcagttattctcatactagatctaaatgtttttctttttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA