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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctatatgccagtttgttttcgtagcattgatctaagtccctttttcccattgtcgttattctgcatatttaaactgttcctaatgtttaattacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGT

Basic information

species Zea mays
transcript GRMZM2G052546_T07
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g01750.5 (Oryza sativa), 3'ss of exon 6
cctatatgccagtttgttttcgtagcattgatctaagtccctttttcccattgtcgttattctgcatattt--aaactgtt-------cctaatgtttaattacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGT
   | |||  | |||   |     |||||||  | | | ||||||  ||||||||  |  | | |||||||  ||| | ||       | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||| ||| |||||  ||||||||| |||||||||||||| |||
--caaatgtaacttttcct-----gcattgacttgaatgcctttt--ccattgtctgttctgtccatattttcaaagtcttaaagtggcataatgtttaattacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGATTAGCAAACTGCACAAGCTTGTCAACCATAATGGTGGGGTAACATATATACACTGT
















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|148952817|gb|EC898809.2|EC898809
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|148970824|gb|EE021591.2|EE021591
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|148967268|gb|EE018472.2|EE018472
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|15427195|gb|BI543017.1|BI543017
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAG
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAG
EST: gi|76290045|gb|DV029613.1|DV029613
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGGTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|21621474|gb|BQ619480.1|BQ619480
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAN                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|149081546|gb|EE170685.2|EE170685
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATT
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATT
EST: gi|71435430|gb|DR816480.1|DR816480
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|67023551|gb|CO452300.1|CO452300
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|76914764|gb|DV165677.1|DV165677
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|74234762|gb|DT642676.1|DT642676
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
EST: gi|148934585|gb|EC878634.2|EC878634
EST:     GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAG                         GGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA
genomic: GATTATTCTCTACAATTCAAAGATATTGTGCACTGCCGTGCGGAAATTAGgtagccaaac ... attacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccattgtcgttattctgcatatttaaactgttcctaatgtttaattacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGT
                                    taatgtttaattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctatatgccagtttgttttcgtagcattgatctaagtccctttttcccattgtcgttattctgcatatttaaactgttcctaatgtttaattacaccagGGATTTTGATGCTTTTGATTTGCGATTGAGGCTTCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG