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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatccttatcccttttctttgaatatgttctagcaaatcacctcgacatatatatttgttaacttcatcaatcgaggattcatgactcataagaccttgtttttatcagGCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGATGAGACCTGTAGCCAGTATGTTATCGATACGAACAACAAGGGTGAAATA

Basic information

species Zea mays
transcript GRMZM2G002361_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002361_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g01130.1 (Oryza sativa), 3'ss of exon 3
gtaaaatccttatcccttttctttgaatatgttctagcaaatcacctcgacatatatatttgttaactt---------catcaat-cgaggattcatgactcataagaccttgtttttatcagGCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGATGAGACCTGTAGCCAGTATGTTATCGATACGAACAACAAGGGTGAAATA
||||  ||  | ||    ||   |||     |  | |  |  ||   |  ||||| |  |   |  |||         ||||| | |   || | |    |  |  | | ||  | |||  |||||||||||||||| |||||| |||||||| ||||| || || |||||||||||| | ||||| || |||||||| || ||  | | ||||||  || | 
gtaacttctctttctacctttgatgatgtcttctttgttagacatgccctcatatctgctaactgcctttacagtttacatcactgcattgactaactgtttgtt-gtcttttctcttaaaagGCATGCACATTATCTAGCTGGTATCACACCCCTTGCACTGGTCTGGAAAGATGAGGCTTGTAGTCAATATGTTATTGACACAGATAGCAAGGGACAAGTC

upper sequence: GRMZM2G002361_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g01420.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaatccttatcccttttctttgaatatgttctagcaaatcacctcgacatatatatttgttaacttcatcaatcgaggattcatgactcataagaccttgtttttatcagGCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGATGAGACCTGTAGCCAGTATGTTATCGATACGAACAACAAGGGTGAAATA
          |||   |  | |||   ||      |  ||| || ||    || | |||||    |  |  |     |    ||      | || | |   | | ||  | |||||||| ||||||||| |||||| |||||| ||  |  | || ||||| ||||||| |||||| |||||||||||||||||  | |  || ||  |  | 
----------tattagtcatttttatgtaccacacatgaaaccaactt---atttctatttcaccatgtattggtaagtttttttcctgatgattatatggtttcttccttagGCATGCGCATTATCAAACTGGAAACACACCACTGACATTGGTTTGGAAGGATGAGAACTGTAGTCAGTATGTTATCGATACAGATAGTAAAGGACAGGTT
















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|60348284|gb|DN215257.1|DN215257
EST:     TACTCAGGCAGCATGCCTTATGTCAAAGATGGTTTGGTGTTCTACAACAA                         GCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGA
genomic: TACTCAGGCAGCATGCCTTATGTCAAAGATGGTTTGGTGTTCTACAACAAgtaaaatcct ... tttttatcagGCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGA
EST: gi|149108582|gb|EE189724.2|EE189724
EST:     TACTCAGGCAGCATGCCTTATGTCAAAGATGGTTTGGTGTTCTACAACAA                         GCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGA
genomic: TACTCAGGCAGCATGCCTTATGTCAAAGATGGTTTGGTGTTCTACAACAAgtaaaatcct ... tttttatcagGCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttaacttcatcaatcgaggattcatgactcataagaccttgtttttatcagGCATGCACATTATCAAGCTGGAATCACACCTCTTGCCCTAGTATGGAAAGATGAGACCTGTAGCCAGTATGTTATCGATACGAACAACAAGGGTGAAATA
  tgttaac  putative branch site (score: 2)
                                        ccttgttttt  putative PPT
                                          ttgtttttat  TA-rich tract