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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatggttgcattttcttgaattaatgttaaaaggacaaacatgataaatagtgtaatatttttggtatgctcaccatgattcttttctgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG

Basic information

species Zea mays
transcript GRMZM2G344476_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G344476_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g47120.1 (Oryza sativa), 3'ss of exon 6
ttgcatggttgcattttcttgaattaatgttaaaaggacaaa-catgataaat--agtgtaatatttttggtatgctcaccatgattcttttctgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG
|| ||   |   ||||    |    || |  ||||        ||    || |  | | |||   | |     | |||||  | ||  || ||| |  ||||||||||||| |||||||||||||||||||| | |||||| |||||||||||||||||||||||||| || || ||||||
ttacacc-tcctatttataagtggaaagggcaaaatattttgtcacagcaagtcaaatttaagtctgtaaactttctcactgtaatcattatcttt--tttagGTCGATATCTTCCGTGGGTTTACTTTGCCAGGAGCTCCGACTTTTAGGCAAGTTTTTGGAGGACAGTTGATAGGACAG
















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|50337659|gb|CO532785.1|CO532785
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|148956464|gb|EC902291.2|EC902291
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|74238643|gb|DT646557.1|DT646557
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTTCGTGGGTTTTACTTTGCCCGAAGCTCCA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTT-ACTTTGCCGGAAGCTCCA
EST: gi|211119071|gb|FL021982.1|FL021982
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|149104205|gb|EE289638.2|EE289638
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTT
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTT
EST: gi|148936448|gb|EC880552.2|EC880552
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|149112589|gb|EE191373.2|EE191373
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|50331303|gb|CO526429.1|CO526429
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|148958992|gb|EE010517.2|EE010517
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|148944150|gb|EC889238.2|EC889238
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
EST: gi|71315960|gb|DR794668.1|DR794668
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCTACTTT
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTT
EST: gi|91875931|gb|EB405888.1|EB405888
EST:     CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAG                         GTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA
genomic: CACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAA

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: 47 (upstream exon), 46 (downstream exon)
Score: 35

TCAATATGGACATTTGTTACAACCAAAAACAATATGGAATGCAGAGGAAACACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 105

TCAATATGGACATTTGTTACAACCAAAAACAATATGGAATGCAGAGGAAACACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

TCAATATGGACATTTGTTACAACCAAAAACAATATGGAATGCAGAGGAAACACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 63

TCAATATGGACATTTGTTACAACCAAAAACAATATGGAATGCAGAGGAAACACCTGAACATTCTTTGCTGGAACAAATTTTGCACTTAGAACCACTAGAGgtaagtataa ... tgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataaatagtgtaatatttttggtatgctcaccatgattcttttctgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG
                         tgctcac  putative branch site (score: 63)
                                     ttcttttctgtgtttt  putative PPT
     atagtgtaatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatggttgcattttcttgaattaatgttaaaaggacaaacatgataaatagtgtaatatttttggtatgctcaccatgattcttttctgtgttttagGTCGATATTTTCCGTGGGTTTACTTTGCCGGAAGCTCCAACTTTTAGGCAAGTTTTTGGAGGACAATTCATTGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
-tgcatgg
- - - - ttgcatt
- - - - - - - - -cttgaat
- - - - - - - - - - - - - - - - - - -acaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgct