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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggctattacattgctttgcatttctggtggtccttttttttgtgctctgtaatacctattatgtgttcattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 34
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 34
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 32
---------------------------------------------------------gtacggctattacattgctttgcatttctggtggtccttttttttgtgctctgtaatacct----attatgtgttcattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGG--CTGAAGT-TGCT
                                                            | |  |    ||||      |   ||     |  || ||||     |||| |||   |    |||   ||||| |  |||||||||| |||||||| |||||||||||||| || ||||||||| | ||  | || ||||| || | || |||   ||| ||||||| |||  |||||   ||  
gtacatccttggcagattaatacggatggtcatgggatgtctgcccctagttggacaaacccgagagagaattgtaacctaccactacaactatttcttttctgtttctggaatgtttgctaattgcatgttcttcatgcagAACCGCCATTCATTTGAGAGACCTGTAAAGATCTATAACTAGACTTGAGA-AATTTGAGTGACGTGCCGCCATCCAACACCAAGCAAGGGCCTGAAAAGTG--
















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|211450914|gb|FL439857.1|FL439857
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|60348260|gb|DN215233.1|DN215233
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|60400274|gb|DN233081.1|DN233081
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|78106266|gb|DV524684.1|DV524684
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|60394863|gb|DN227732.1|DN227732
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|211112821|gb|FL033799.1|FL033799
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|67014431|gb|CO443180.1|CO443180
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
EST: gi|67020350|gb|CO449099.1|CO449099
EST:     GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAG                         AACCGGCATTCATTTGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG
genomic: GACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAG

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), 48 (downstream exon)
Score: 184

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 134

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 105

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 119

AGAAACATGTATGGAGCTTGGGAGCAGTATCTTGGACTGGAACATCCGGACACGGCTCCTAGGAAGGCACACACGGCTAATCAGgtacggctat ... cattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggtggtccttttttttgtgctctgtaatacctattatgtgttcattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT
                                           ttcatttt  CT-rich tract
           ttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggctattacattgctttgcatttctggtggtccttttttttgtgctctgtaatacctattatgtgttcattttgcagAACCGGCATTCATTCGAGAGACCTGTAAAAATTTATAACTAGGCATGTTAGAAATTGAGCGATGAGCTGCCGCTCAATACCAAGCCAGGCTGAAGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG