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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcattaaagatgttaagacttcgcacagtcttaaacagtaggaattacatggtaacagtttttgagcattcagattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT

Basic information

species Zea mays
transcript GRMZM2G056975_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 9
ctgcattaaagatgttaagacttcgcacagtc-ttaaacagtaggaatta--catggtaacagtttttgagcattca---gattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT
       |||||  |  |  |  |  | | |  ||||    ||| | |||  | ||   ||  ||||| |     |    | |||| ||  | || | ||||||||| ||||||||||||||||||||||||| ||||| || |||||||| || ||||| || ||||||||||||||  | ||||||||||||||||||||||||
------aaaagaactagatgcaacaaaaaattgttaagttatagtacttaaccgtgaagaccttttttcattgcacgaagggttaatttttaatttgataatgcagGCTGGGTTCACTGACATTCAAAGCTCCTGACAATGTGAAATACCCGTCGATGGATCTCGCCTATGCAGCTGGAAGAGCTGGGGGCACCATGACAGGAGTT

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------------------------------------ctgcattaaagatgttaagacttcgcacagtcttaaacagtaggaattacatggtaacagtttttgagcattca--gattaagttccagttg-gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT
                                                                                        ||   || || | | ||   ||    |  |  |    | |   ||||  ||     |   |||  |  ||  |  | |    ||  || || | | || |||| | |||||||| ||||| ||| |||| || || ||||| || ||||| ||| | || |||||||| |||||||| ||||| ||||| ||||||||||||
gtactatattctttccctgcagcttactaatttcaactctatcaaattctatcttcagtccataccaaagaaaatagacagatccagttgatatagagttttcaaattttgaagcctttatgttgaatgaaaattttatctagtccaatttgaattatcgatggttcttatttgaggtgtgattatccagGATTGGTTCACTTACATTTAAAACTCCAGATAATGTAAAGTATCCATCCATGAATCTTGCCTATGCTGCTGGCCGTGCTGGAGGCACAATGACAGGAGTT

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 10
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 10
---ctgcattaaagatgttaagacttcgc-acagtcttaaacagtaggaattacatggtaacagtttttgagcattcagattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT
   |   |||||| |  | || |    |  | | |  | || | | | ||| |  |  ||  |||||    | |      | || ||  | | |  |  |||||| | || ||||||||||| ||| |||| ||||| || ||||| ||||| ||||| || |||||||| ||||| |||||||| ||||||||||||||||||
tttccagattaaaca-ataaatatggtgtgaaaataatgaaaacttgcaatcagtt--tattagtttgcttg-acatgattgaaattggaatggaatggtgcagGCTTGGGTCACTGACATTTAAAACTCCTGACAATGTGAAATATCCATCCATGGATCTTGCCTATGCTGCTGGACGGGCTGGAGGCACCATGACAGGAGTT

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|16379495|gb|BI992983.1|BI992983
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|14244555|gb|BG840684.2|BG840684
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|31362671|gb|CD447028.1|CD447028
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCCCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAGAGCTCCAGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|67032629|gb|CO461378.1|CO461378
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCCCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAGAGCTCCAGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|84970217|gb|DW468567.1|DW468567
EST:     GATAGAATCTATTGTTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|18167286|gb|BM337125.1|BM337125
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAATCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|71445034|gb|DR826084.1|DR826084
EST:     GATAGAATCTATTGTTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|89252718|gb|DY624504.1|DY624504
EST:     GATAGAATCTATTGTTCTGAGGTCACCGGGCCTCGTCTGGATCTTTGCAA                         GTGGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|86474441|gb|DY240811.1|DY240811
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|12968309|gb|BG265255.1|BG265255
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTTAAATACCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT
EST: gi|211274635|gb|FL463120.1|FL463120
EST:     GATAGAATCTATTGCTCTGAGGTCACCTGGCCCCGTCTGGATCTTTGCAA                         GTTGGGTTCACTGACATTCAGAGCTCCAGACAACGTWAAATMCCCATCAAT
genomic: GATAGAATCTATTGCTCTGAGGTCACCTGGCCTCGTCTGGATCTTTGCAAgtatgacatc ... gttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacatggtaacagtttttgagcattcagattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT
                              attaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcattaaagatgttaagacttcgcacagtcttaaacagtaggaattacatggtaacagtttttgagcattcagattaagttccagttggttaatgcagGTTGGGTTCACTGACATTCAAAGCTCCCGACAACGTAAAATACCCATCAATGGACCTAGCCTATGCAGCTGGCCGGGCTGGGGGCACCATGACAGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG