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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttttctttcctgttatttttttggaagtttataaagtctatcctttagctactgcacatggcctaaaaaactaaagcatttcgttctcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC

Basic information

species Zea mays
transcript GRMZM2G074466_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 30
------ttttttttctttcctgttatttttttggaagtttataaagtctatcctttagctactgcacatggcctaaaaaactaaagcatttcgttctcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC
      | |  | |    ||||||| |   |   |    ||| || |    | | | |    || || |||      | | |  |||||||   | ||| ||  ||||||||||| ||| |||||||| ||||| |||||| | ||||| |||||||||||||||||||||||||| |||||||  || ||||||||||| || ||
cagtactatgatctaccacctgttagtgcataaaagagatatcaaattatacatgtgg----tgaac-tggtgattgatagtccagcattttcat-tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGTCCATTAGTGCCAGTGATCATTGGCTAGGAATAGGTGCTGCTGACAACTC

upper sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 29
------ttttttttctttcctgttatttttttggaagtttataaagtctatcctttagctactgcacatggcctaaaaaactaaagcatttcgttctcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC
      | |  | |    ||||||| |   |   |    ||| || |    | | | |    || || |||      | | |  |||||||   | ||| ||  ||||||||||| ||| |||||||| ||||| |||||| | ||||| |||||||||||||||||||||||||| |||||||  || |                
cagtactatgatctaccacctgttagtgcataaaagagatatcaaattatacatgtgg----tgaac-tggtgattgatagtccagcattttcat-tctcttgtagGAGGAATAAGATGTGTCAAGAACCTTACGCTTCACTCGGCATCTGTTCTGTCCATTAGTGCCAGTGATCATTGGCTAGGAATAG----------------
















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|32933778|gb|CF038590.1|CF038590
EST:     GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG                         GAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
genomic: GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
EST: gi|67010825|gb|CO439574.1|CO439574
EST:     GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG                         GAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
genomic: GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
EST: gi|71331763|gb|DR802742.1|DR802742
EST:     GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG                         GAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
genomic: GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
EST: gi|32850651|gb|CD990332.1|CD990332
EST:     GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG                         GAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
genomic: GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
EST: gi|60354992|gb|DN221965.1|DN221965
EST:     GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG                         GAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
genomic: GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
EST: gi|211489770|gb|FL012891.1|FL012891
EST:     GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG                         GAGGAATNAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT
genomic: GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGT

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), 45 (downstream exon)
Score: 122

GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 111

GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 113

GTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAGgtgagttctt ... tcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttagctactgcacatggcctaaaaaactaaagcatttcgttctcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC
                           aactaaa  putative branch site (score: 113)
                                   catttcgttctctttt  CT-rich tract
                      taaaaaactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttttctttcctgttatttttttggaagtttataaagtctatcctttagctactgcacatggcctaaaaaactaaagcatttcgttctcttttacagGAGGAATAAAATGCGTCAAGAATCTTACACTTCACACAGCATCCGTTCTGTCCATTAGTGCCAGTGATCACTGGCTAGCGATTGGTGCTGCTGATAATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaaa