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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcag

Basic information

species Zea mays
transcript GRMZM2G135132_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 8
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcag
| ||||| ||||||||||||||||||||||| |||||||| ||||| || || |||||||| ||| | ||||||||||||||||| || || |||||||||||||| ||  | ||  | | | ||  ||||||| ||| ||  ||||||| | ||| |  | |||||||
TGGAGAAAGCAAAATACATCTACATTGCTGGCTTTTTCCTTACGGTCTCCCCAGATTCTATTCAGCTTGTTGCTGAGCATGCTGCCGCTAACAACAAGgtaaattc-tatcacta-aagagttccctttgaagtggtttttagagtttgactaaccgtgttgttttcag

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G36630.1 (Glycine max), 5'ss of exon 8
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcataataatatgaaaatgccagttgaagttgt-tgttttagtttgattgaccattctattttcag------
|||| ||||| || || || || ||||| || ||||||||||| || ||||| ||||| ||||||||||||||||||||| |||| |||||||||||||| ||   |||  | ||  ||| |||   ||    ||   ||  |   | ||||     ||| ||||           
TTGAAAAGGCCAAGTATATTTATATTGCCGGCTTTTTCCTCACTGTATCACCAGATTCCATCCAGTTAGTTGCTGAGCATTCTGCTGCAAATAACAAGgttaa---atatgattagaaaattgcttctttctattaaatggctgtttctgatgctttattttattcctgtatgcag

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G06580.1 (Glycine max), 5'ss of exon 8
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgt-aaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcag------
|||| ||||| || ||   ||||||| |||| ||||||||||| || || |||||||| || || || |||||||| ||||| || |||||||||||||| | ||      | |  |    || || |||  | | |  ||||| |   |||| |  |||||||||          
TTGAAAAGGCCAAGTATTACTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTGGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatgatttgaacttggcattcctgttttactggcagtttttg--agattaagtattctatttctgtatgcag

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 8
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgt-aaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcag------
|||| ||||| || ||  |||||||| |||| ||||||||||| || || |||||||| || || ||||||||||| ||||| || |||||||||||||| | ||      | |  |    || || |||  | | |  ||||  |   ||||     |||||||           
TTGAAAAGGCCAAGTATTTCTACATTTCTGGCTTTTTCCTCACTGTATCTCCTGATTCCATACAATTAGTTGCTGAACATGCAGCTGCAAATAACAAGgttagatatgatttgaacttggcattcctgttttactagcagtttctg--agattagttgttctattcctgtatgcag

upper sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G33910.3 (Glycine max), 5'ss of exon 5
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcag------
|||| ||||| || || || || |||||||| ||||||||||| || ||||| ||||| |||||| ||||||||||||||||||| |||||||||||||| ||   |||  | |   ||| |||   ||    ||      |   | ||||     ||| ||||           
TTGAAAAGGCCAAGTATATTTATATTGCTGGGTTTTTCCTCACTGTATCACCAGATTCCATCCAGCTAGTTGCTGAGCATGCTGCTGCAAATAACAAGgttaa---atatgattggaaaattgctgcttcctattaaatgctgtttctgatactttattttattcctgtatgcag

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|4775994|gb|AI664997.1|AI664997
EST:     CTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATANCAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTGTGAT
genomic: CTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|211535004|gb|FL000873.1|FL000873
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCATCC-TTCATCTGTGAGTTTTTCTATGA
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGC-TCCCTTCATCTGTGAGTTTTTCTATGA
EST: gi|60340226|gb|DN207199.1|DN207199
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|211259748|gb|FL311234.1|FL311234
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|60355835|gb|DN222808.1|DN222808
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|211430957|gb|FL254719.1|FL254719
EST:     ACCTGATTCTATCCCAGT-AGTTGCTGAGCATGCTGCGGCAAATAACA-G                         GTGTTCCTGATGAACCTCTCTGCTCCTTTCATCTGTGAGTTTT-CTATGAT
genomic: ACCTGATTCTATCC-AGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|211430954|gb|FL254716.1|FL254716
EST:     ACCTGATTCTATCCAGTTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTTGTTCCTGAATGACCCTCTCTGCTCCCTTCATCTGTTGAGTTTTTCCTA
genomic: ACCTGATTCTATCCAGTT-AGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGT-GTTCCTGA-TGAACCTCTCTGCTCCCTTCATCTGT-GAGTTTTTC-TA
EST: gi|60337076|gb|DN204049.1|DN204049
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|31353988|gb|CD438345.1|CD438345
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
EST: gi|60395531|gb|DN228401.1|DN228401
EST:     CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAG                         GTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT
genomic: CACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 62

TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC


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

TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 123

TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcat ... ctattttcagGTGTTCCTGATGAACCTCTCTGCTCCCTTCATCTGTGAGTTTTTCTATGATGCCCAAGAGAAGGTCCTCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGAGAAGGCAAAATACATCTACATTGCTGGATTTTTCCTCACGGTGTCACCTGATTCTATCCAGTTAGTTGCTGAGCATGCTGCGGCAAATAACAAGgtaaattcataataatatgaaaatgccagttgaagttgttgttttagtttgattgaccattctattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC