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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT

Basic information

species Zea mays
transcript GRMZM2G176604_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g03410.1 (Oryza sativa), 3'ss of exon 1
--cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
  | | ||| |    |||  | |    | |   |||   |  |   || | |  |  || ||| ||| ||||  |       ||  ||| ||      ||||||||||||| ||||||||||||||||||||||| ||||| || || ||||||||||| || |||||||| || ||||| || ||||| ||||| || |||
cacggctttctagggactggattaccgtttc--attttctcacacattttcttgttctgttttatgacaacaaaaaatcaaattgttttcctgctttgccagGGGCCAGGCTGAGAAGGAGTTCAAGGTGGAGGTTGAAGCGATCGGGCGTGTTCGGCATAAGAATCTCGTTAGATTGCTCGGCTACTGTGTAGAGGGCGCT

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G03650.1 (Glycine max), 3'ss of exon 1
cagatttttgaatactacactgtt-ctctaggattgggttgccgt--ttatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
    | ||||| ||||  |||||| || ||   |  |  |   ||  |  | | ||  |  ||      |  | ||    |||  | |||     |    ||||||||| || ||||  || || || || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| || || || |  
--tttctttgattact-tactgttgctgtatagtgagaataatgtgatcttgtgattgtctttctcttaagaagtaagtgcttaatatttaactcattttcagGGGCCAAGCTGAGAGAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGTGTGCGGCACAAGAATCTTGTTAGGTTGCTTGGATACTGTGTTGAGGGGGAA

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G07250.1 (Glycine max), 3'ss of exon 2
--cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
  ||    |||   |  |  | |  |  ||     ||  | |  |   ||    | || |||     |  | || ||  |||  | |||     |    ||||||||| || ||||  || || || || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| || || || || 
tccattactttctttctttgattacttactgttgctgtatagt-gagaatgatgtgat-cttgtgattgtctttctctgcttaatatttaactcattttcagGGGCCAAGCTGAGAGAGAATTTAAAGTTGAGGTAGAAGCAATTGGTCGTGTGCGGCACAAGAATCTTGTTAGGTTGCTTGGATACTGTGTTGAGGGGGCA

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 1
cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctt---tctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
   ||||    ||   |   || | |||||    |  || ||| |  |    |  |  ||   |     |  | ||   || |  |||||     |    |||||| || || ||||| || || || || ||||| |||||||||||||| || || ||||||||||| || ||||||||||| ||||| || || || || 
---atttgattatttcatgttgctatctagtgaagttttcccggtcctggtcttgtatttgtcttcctcagaaataaatacctcatgtttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 1
cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
  |||| ||  ||  | |  | |  |  ||  || |    ||   | ||  ||    |||||| |    | ||   ||||  |||||          |||||| || || ||||| || || ||  | ||||| |||||||||||||| || || ||||||||||| || ||| ||||||| ||||| || || || || 
ttgattattacatgttgctatctagtgaagttttcgtggtcctggtcttgtatttgtctttctcagtgaaataaatacttcatgtttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34699 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------cagatttttgaatactacactgttctctaggattgggttgccgtttatttca---tcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGG-TGCT
                                                                           |   |  |  |   |    ||||  || | |      ||||  | |||  ||    | || | | |  ||| |  |||   |||   | || |       ||| |||||||||||||| ||||| | |||||| || ||||| |||||    || || ||||| ||||| |||||||||||||| |||||||  ||  | ||| 
gtaagtctctctctccttctctctcgctcggattggatttgcttgcgctctggcattctcgcgatctatggcgttcttgtgatccatggcattcctgtgatccatggcattcttgcgatctatgccaagtccttgatcttttgtaaaacgatc---tttccatcttttttgctcgcagCGGCCAGGCCGAGAAAGAGTTTAGGGTGGAAGTGGAAGCGATTGGAAAGGTGCGTCACAAGAATCTGGTCAGGTTGCTTGGCTACTGCGCCGAGAGCTGC-

upper sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ31013 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------cagatttttgaatactacactgttctctaggattgggttgccgtttatttca---tcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGG-TGCT
                                                                           |   |  |  |   |    ||||  || | |      ||||  | |||  ||    | || | | |  ||| |  |||   |||   | || |       ||| |||||||||||||| ||||| | |||||| || ||||| |||||    || || ||||| ||||| |||||||||||||| |||||||  ||  | ||| 
gtaagtctctctctctttctctctcgctcggattggatttgcttgcgctctggcattcttgcgatctatggcgttcttgtgatccatggcattcctgtgatccatggcattcttgcgatctatgccaagtccttgatcttttgtaaaacgatc---tttccatcttttttgctcgcagCGGCCAGGCCGAGAAAGAGTTTAGGGTGGAAGTGGAAGCGATTGGAAAGGTGCGTCACAAGAATCTGGTCAGGTTGCTTGGCTACTGCGCCGAGAGCTGC-

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|149071431|gb|EE159826.2|EE159826
EST:     CGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAAG                         GGGCC-GGCCG
genomic: CGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATA-Ggtactacact ... caaacaccagGGGCCAGGCCG
EST: gi|148973240|gb|EE024318.2|EE024318
EST:     ACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAG                         GGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAACAATTGGTCGTGT
genomic: ACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGT
EST: gi|76915910|gb|DV166163.1|DV166163
EST:     CGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCCTCA-TAATAG                         GGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCTATTGGTCGTGT
genomic: CGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCC-TCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGT
EST: gi|71322783|gb|DR798077.1|DR798077
EST:     ACGCTGCACGACTCCACTTTGATCGCCGTCTAGAATCTCCTCAATAATAG                         GGGCCAGGTCGAGAAGG
genomic: ACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGG

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: 164

CCGAGGAGAATGTCATCGGGGAGGGTGGCTACGGGATCGTGTACAAGGGCACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 186

CCGAGGAGAATGTCATCGGGGAGGGTGGCTACGGGATCGTGTACAAGGGCACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

CCGAGGAGAATGTCATCGGGGAGGGTGGCTACGGGATCGTGTACAAGGGCACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 702

CCGAGGAGAATGTCATCGGGGAGGGTGGCTACGGGATCGTGTACAAGGGCACGCTGCACGACTCCACTTTGATCGCCGTCAAGAATCTCCTCAATAATAGgtactacact ... caaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
                 tgataac  putative branch site (score: 702)
                         ttatccactttttgtt  CT-rich tract
                   ataacattat  TA-rich tract