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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcttaacttttatctttaagctgtcctctatttatgtggaatcaatggagaataaagttatgtactagttttgattttcatatttcatgattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTTCGAGTGGAAACCTGGGAGGATAACTCATGGCGTAAAATGAAGTTCAGGA

Basic information

species Zea mays
transcript GRMZM2G044569_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044569_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g29590.1 (Oryza sativa), 3'ss of exon 3
tatcttaacttttatctttaagctgt-cctctatttatgtggaatcaatgga---gaataaagttatg-tactagttttgattttca--tatttcatgattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTTCGAGTGGAAACCTGGGAGGATAACTCATGGCGTAAAATGAAGTTCAGGA
      || | | || ||  || |||   | | | | ||    ||   |  |   ||||  ||  |   ||| | || ||||||||   || | | | ||||| ||||||||||||||||||||||| |||||||| ||||||||||| || ||||| ||||||||||| |||||||| || ||||||||||||||||||||| |||
------aaatgtaattttctaggtgtgtttttttctttgcaacatgttttaacctgaatggagaaagaataccaattctgattttctattaatgcttaatttt-tagGAAGGATTTGCATTTTCACATTGCACAACATGCAAAGCTCAATTCCATCTCCGAGTGGAAACTTGGGAGGACAATTCATGGCGTAAAATGAAGTTCCGGA

upper sequence: GRMZM2G044569_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S243_90V6.1 (Physcomitrella patens), 3'ss of exon 2
tatcttaacttttatctttaagctgtcctctatttatgtggaatcaatggaga-ataaagttatgtactagttttgattttcatatttcat--gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTTCGAGTGGAAACCTGGGAGGATAACTCATGGCGTAAAATGAAGTTCAGGA
 ||    || ||| || |  | |||   | |     | ||| |   | |      |   | ||| |  |  || |   | | || ||  ||  ||  ||||||||||| ||||||||||  || ||||||||||||||  |||  | |||  |  ||||  | | |   |  || |     ||| | | | | |||||| |  
gatgaagacctttttcatggaactgaaatgt---cgtatggtacttacgctcttgttctgatatttgatgcttgtcgatctgatgttgtatttgaaattgtagGAAGGTTTTGCATTTTGCCATTGCACAACTTGCAAGACTCCATATCAAATCAGAGTCCACATCCCAGCTGACAGAGAGTGGAGGACACTCAAGTTCCGCT
















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|47962587|gb|CN845296.1|CN845296
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|78085525|gb|DV513918.1|DV513918
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|71766873|gb|DR964810.1|DR964810
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|71764260|gb|DR962197.1|DR962197
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|89253176|gb|DY624962.1|DY624962
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACATCTTGCAGAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|71449470|gb|DR830520.1|DR830520
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|78075719|gb|DV504153.1|DV504153
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|78085425|gb|DV513818.1|DV513818
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|74242907|gb|DT650821.1|DT650821
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|91875640|gb|EB405597.1|EB405597
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|149051784|gb|EE155909.2|EE155909
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|76287272|gb|DV026840.1|DV026840
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|211220736|gb|FL455232.1|FL455232
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATYTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|91877670|gb|EB407627.1|EB407627
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|26457371|gb|CA828954.1|CA828954
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|67025393|gb|CO454142.1|CO454142
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
EST: gi|211122360|gb|FL034211.1|FL034211
EST:     CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAG                         GAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT
genomic: CTCAGCAGTTTGTTCACCGTTCTTGTCTTGACCACTGGCGATCTGTTAAGgtacacccag ... gattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggagaataaagttatgtactagttttgattttcatatttcatgattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTTCGAGTGGAAACCTGGGAGGATAACTCATGGCGTAAAATGAAGTTCAGGA
                         ttttgat  putative branch site (score: 4)
                              attttcatatttcatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcttaacttttatctttaagctgtcctctatttatgtggaatcaatggagaataaagttatgtactagttttgattttcatatttcatgattttgtagGAAGGATTTGCATTTTCACACTGCACAACTTGCAAAGCTCAGTTTCATCTTCGAGTGGAAACCTGGGAGGATAACTCATGGCGTAAAATGAAGTTCAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT