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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattgtagaaattcgtttgtgtttctgcaagatcctgtgtaagttataatgctttgctcatgttcagtcacgtgatcttattagtctattgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG

Basic information

species Zea mays
transcript GRMZM2G126517_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126517_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g39420.1 (Oryza sativa), 3'ss of exon 6
----atattgtagaaattcgtttgtgtttctg-caagatcctgtgtaagttataatgctttgctcatgttcagtcacgtgatcttattagtctattgcat-gacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG
     |||  | |||||| | | || |||||| | ||    |        |  |||| | |  |  || ||| ||   |       |||    ||||||| | ||||||||| |||| || || ||||||||||||| ||||||||||||||| || ||||| |||||| | || |||||  ||
tgtgctatatttgaaatttggt-gtatttctggctaggcatttcaatgaatgcaatgttgt-ttggtgctcaatcgtatag----gttaactgattgcattggcagGAAACTCAAGGAGTAACGGTTGCTGCTTACAAAACCAATGAATTTCCTGCTTTCTTTACAGAAGTCAGCGGATGTAAG
















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|67038503|gb|CO464823.1|CO464823
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|149082843|gb|EE172069.2|EE172069
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|149015839|gb|EE045506.2|EE045506
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|211152952|gb|FL361222.1|FL361222
EST:     CG-CAGGTGTGAAGTCCATTT-GGACATACCGCGGACACTTGA-TACCTG                         AAAACTGA-GGG-TGACTGT
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGT
EST: gi|31355893|gb|CD440250.1|CD440250
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|78085709|gb|DV514102.1|DV514102
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAG
EST: gi|88748923|gb|DY533064.1|DY533064
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|74236391|gb|DT644305.1|DT644305
EST:     GTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGTTGCTTACAGAACCAATGAATTTCCCGCG
genomic: GTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|74236392|gb|DT644306.1|DT644306
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGTTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|31355559|gb|CD439916.1|CD439916
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
EST: gi|71764027|gb|DR961964.1|DR961964
EST:     CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTG                         GAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG
genomic: CGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCG

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

TGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTGTTGTATCGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 111

TGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTGTTGTATCGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

TGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTGTTGTATCGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

TGTCTCCTCAGACTTAACTGAACTTGGAAAGACTCCTGTAGCTGTTGTATCGGCAGGTGTGAAGTCCATTTTGGACATACCGCGGACACTTGAATACCTGgtagtatact ... tgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataatgctttgctcatgttcagtcacgtgatcttattagtctattgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG
                              atcttatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattgtagaaattcgtttgtgtttctgcaagatcctgtgtaagttataatgctttgctcatgttcagtcacgtgatcttattagtctattgcatgacagGAAACTGAAGGGGTGACTGTTGCTGCTTACAGAACCAATGAATTTCCCGCGTTCTTCACAGAAATTAGTGGATGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - -gatcctg