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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctaccgccgccgctttctacaccttctcttgtcttgatcctccacgtctttgctcatcccgatgtggctgatctccaccgcttctctgggatctttttcgctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG

Basic information

species Zea mays
transcript GRMZM2G113720_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113720_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g49030.1 (Oryza sativa), 3'ss of exon 1
gtaagcctaccgccgccgctttctacaccttctcttgtcttgatcctccacgtctttgctcatc-ccgatgtggctgatctc-caccgcttctctgggatctttttcgctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG
|||||| |  |  ||||||   |  | ||| |||   ||  | |||  |    | | |  | |  | ||| |    | |  |       |    || ||  |||| ||   ||| ||||||||||||||||||||||||||||||||||| ||||||||   ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
gtaagcttctcctcgccgccgccgccgcctcctccc-tcgcgttccgtcgatccatcgagcgtggctgatctcttcgtttccgtgtttgtgtgttgcgaatttttccggcggcg-cagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTCCCGACCCCCGGCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTCCGCG

upper sequence: GRMZM2G113720_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S74_193V6.2 (Physcomitrella patens), 3'ss of exon 1
gtaagcctaccgccgccgctttctacaccttctcttgtcttgatcctccacgtctttgctcatcccgatg--tggctgatctccaccgcttctctgggatctttttcgctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG
           |     | ||  |  |  |   | |    ||| ||  || |   |  ||  |    ||   |  | | |    | |||| |      || | ||| |   |   ||||| ||||| ||||||||||| || || || || || ||| | ||| |||||   || |||   ||||||||||||||||||||||||||||| || ||||
----------tgtgtatgattgtttgatgtcaccgtagtatgacccatcatgcggtaacttgttttcatcattttccggttctgatcgctcc-----aatttcttttg---gtatcagTTTCATCAATACCAGGTGGTTGGGCGGGCCCTTCCTACCGCGACCAATGAGACACCTAAGGCTTACCGCATGAAGCTCTGGGCCACCAACGAAGTGCGCG

upper sequence: GRMZM2G113720_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ38689 (Selaginella moellendorffii), 3'ss of exon 1
gtaagcctaccgccgccgctttctacaccttctcttgtcttgatcctccacgtctttgctcatcccgatgtggctgatctccaccgcttctctgggatctttttcgctcgcg-gcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG
                                                 | |  || |  || | ||| | |   ||||  || || ||      ||||  |  |  |  |  |||||| ||||||||||||||||| ||  | ||    || || ||   | |||||||||| ||||| ||||| |||||||||||||||  | |||| || ||||
-----------------------------------------------gtaagaattcg--cagctcga-gcgctcgatc--catcgatt------gatccctcccattgtctcgcagTTTCATCAGTACCAGGTGGTCGGGAGAGCTACTCCCACTCCCGACAATGAGCACCCAAAGATGTACCGGATGAAGCTCTGGGCCGGCGACGAAGTGCGCG

upper sequence: GRMZM2G113720_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ31458 (Selaginella moellendorffii), 3'ss of exon 1
gtaagcctaccgccgccgctttctacaccttctcttgtcttgatcctccacgtctttgctcatcccgatgtggctgatctccaccgcttctctgggatctttttcgctcgcg-gcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG
                                                 | |  || |  || | ||| | |   ||||  || || ||      ||||  |  |  |  |  |||||| || |||||||||||||| ||  | ||    || || ||   | |||||||||| ||||| ||||| |||||||||||||||  | |||| || ||||
-----------------------------------------------gtaagaattcg--cagctcga-gcgctcgatc--catcgatt------gatccctcccattgtctcgcagTTTCACCAGTACCAGGTGGTCGGAAGAGCTACTCCCACTCCCGACAATGAGCACCCAAAGATGTACCGGATGAAGCTCTGGGCCGGCGACGAAGTGCGCG

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|211456092|gb|FL381470.1|FL381470
EST:     CTTCGGCGTCCCTCCGGCCACGTGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
genomic: CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
EST: gi|211496031|gb|FL376604.1|FL376604
EST:     CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
genomic: CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
EST: gi|211026951|gb|FL376198.1|FL376198
EST:     CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCC-AACCG
genomic: CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCG
EST: gi|161588806|gb|EY963273.1|EY963273
EST:     CGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCGACCGATGAG
genomic: CGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
EST: gi|211429171|gb|FL408890.1|FL408890
EST:     CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCC-AACCGATGAG
genomic: CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
EST: gi|211453738|gb|FL373101.1|FL373101
EST:     CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCMGACCCCAACCGATGAG
genomic: CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
EST: gi|211449475|gb|FL373075.1|FL373075
EST:     CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGG                         TTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG
genomic: CTTCGGCGTCCCTCCGGCCACGCGAGCTCGCCGAAATGGTCGCCCACAGGgtaagcctac ... ctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccgatgtggctgatctccaccgcttctctgggatctttttcgctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG
          ggctgat  putative branch site (score: 4)
                                    tctttttcgctcgc  putative PPT
                                   atcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctaccgccgccgctttctacaccttctcttgtcttgatcctccacgtctttgctcatcccgatgtggctgatctccaccgcttctctgggatctttttcgctcgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC