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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG

Basic information

species Zea mays
transcript GRMZM2G169914_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g19460.1 (Oryza sativa), 3'ss of exon 2
---agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgc-ttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
    |   | | ||  ||   | || ||| |  |    || |   || ||     | || || | | ||  | | |     | |  |  | ||| ||||| ||||||| |   | |||||||| ||||| |||||||||||||| |||||| | |||||||||||||||||||| ||||||||||||
tcagggaatgtgtaaacattggatg-attcaattagcaggaacgaaaagtta---tagtagtacatctggtttagtcaagcttatatagccttttcaatttcagAGGGTGTAATAGCTGGAGGTGCTGCCGGTGTTGTTGTTGAGACAGCTCTGTATCCTATTGATACAATAAAAACCAGGCTTCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G36580.3 (Glycine max), 3'ss of exon 3
----agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
    | |  |  |   | | ||  |   | ||   || |  | ||| ||  |    | |||||        || ||  | |     |   |  |  |||| |||| ||   | | |||||||| ||||||||||||||||| |||||||||||||| || |||||||| || || ||  | || |||
ggctataagttgcatcttatcacatatgtcta---ttgtcttgtactattaatatattgttgtgggacatacttatgagttatgaatat-tgatctaattgcagATGGTTGCATTGCTGGAGGTGCTGCTGGTGTTGTTGTAGAAACAGCTTTATACCCCATTGATACCATCAAAACTCGACTACAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 2
-agagttctctattcagcagttggatttagatttatggtatacaatgtaggct-tggttgtccttatgcctca-tttgcttgacgtgccttttacaattc-cagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
 | |||  | |||      | |   || |    ||    |||| || ||     ||| | |  |||    ||| |||   ||| | ||    |  ||||  ||||||| |   | || || ||  | ||||| ||||||||||||||||||||||| || ||||| |||||||| ||  | || |||
aatagtattttatcttcttgctaagttca----tagacaatactatatacttgatggattttattacatttcaatttttctgatgagctagatggaatttgcagAGGGCGTTATTGCAGGTGGTACAGCTGGAGTTGTTGTTGAAACAGCTTTATACCCAATTGACACAATAAAAACACGTCTGCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 3
agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttg--tccttatgcctca-tttgcttgacgtgccttttacaattc-cagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
  | |  | | || | |  || |   ||  ||  |     | | | ||  |||| | |  |  |||    ||| | |   ||| | ||    |  ||||  ||||||| |   | || |||||  | ||||| ||||||||||||||||||||||| || || || |||||||| ||  | || |||
-aaatagtat-tttacctttttg--ctaagttggtaaacaatactatatacttgatgggtttattacatttcaatctttctgatgagctagatgaaatttgcagAGGGCGTTATTGCAGGAGGTACAGCTGGAGTTGTTGTTGAAACAGCTTTATACCCAATCGACACAATAAAAACACGTCTGCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G39460.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------------------------agagttctctattca--gcagttggatttagatttatggtatacaatgtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaat--tccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG----
                                                                                             | |||| | || |  ||   | | ||   |||| || | |  |  |   ||||    ||   || | ||  ||    | | ||     ||   ||  | ||||||||    | || |||||  | ||||| ||||| ||||||||||||||||| || |||||||| || ||||| || ||||||    
gtttgtgtatattttgtcttttggttcatttgcaactattattttatgaatctcatgttctgactcatatacagtccttgtatctgaaaagtaatttctttttttattgctaatagtttggcatttttgctttgaatcggcagcttcag-gtgtctaagtcttgttattcttatgttttggttttgatgatgcagAGGGGTTTATAGCAGGAGGTACAGCTGGAGTTGTAGTTGAAACAGCTTTATACCCAATTGATACTATTAAGACTAGACTTCAGGCAG

upper sequence: GRMZM2G169914_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0157g00180.t01 (Vitis vinifera), 3'ss of exon 2
agagttctctattcagcagttggatttagatttatggtatacaatgtaggcttggttgtcctta-tgcctcatttgcttgacgtgccttt-tacaattccagAGGGGGCCTTG--GCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
    || | ||||      ||   |    | ||      ||  |   |  |  |    | |||| |  || ||     | | ||    || |    ||    || ||| ||||  ||||||||   ||||||||||||||||||| ||||||||||||| |||||||||||||| || || ||||||
----ttttttatttttattttctttgccaaatttcatcttatgacaaaatcacgtccttgcttaatatcttatgcttctaatgttttgttatgggtttttgcagAGGGTCTTGTAGCTGGAGGTATTGCTGGTGTTGTTGTTGAAGCAGCTTTATATCCAATTGATACAATAAAAACTAGACTTCAG

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|76015377|gb|DT942547.1|DT942547
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
EST: gi|211463765|gb|FL048904.1|FL048904
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
EST: gi|211461254|gb|FL048902.1|FL048902
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGCCTTGGSTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTAT
EST: gi|50325535|gb|CO520661.1|CO520661
EST:     GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTG                         AGGGGGCCTTGGCTGG
genomic: GGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGG

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: 106

AATTTTGTAATTGCCGACTGAACCGTGCAGAGAAGTCTTGACAAGCGCATGGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 15

AATTTTGTAATTGCCGACTGAACCGTGCAGAGAAGTCTTGACAAGCGCATGGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 12

AATTTTGTAATTGCCGACTGAACCGTGCAGAGAAGTCTTGACAAGCGCATGGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 59

AATTTTGTAATTGCCGACTGAACCGTGCAGAGAAGTCTTGACAAGCGCATGGGCGGAGGTGGAAATGGGGAATCGTGCGATCTCCTCCAAGTCCTTTTTGgtagggggcc ... acaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggcttggttgtccttatgcctcatttgcttgacgtgccttttacaattccagAGGGGGCCTTGGCTGGAGGAGCTGCTGGTGTTGTTGTTGAAACAGCTTTATATCCTATTGATACAATAAAGACCAGGCTTCAG
                             gcttgac  putative branch site (score: 59)
                                       ccttttac  putative PPT
                                         ttttacaatt  TA-rich tract