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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcctcccttgatagctcttcaacttttttcttgtttttttgaacgtccatcatgtatcatctgtattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 47
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 47
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 46
---------------gtctgcctcccttgatagctcttcaact--tttttcttgtttttttgaacgtccatcatgtatcatctgtattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT
                |    ||   | | ||||| || || |  ||| | |||   ||||  |   | |  |  |    |   | | ||| ||||| || || |||||||||||| | ||||||||||||||||| |||||||||||||| |||||||| || || ||||| || ||||||||||||||||||
gttactgctgttctcctggagcttaatagttagcttttaaatttatttcttttggggttttagata-caagtagatgctttgcatgtcctgcagGGCAGGAGCCGATGACAAGCCACTTAGAATGGTCAAAACTGTGTTGCATGAACTTGTAAAGCTTCGTGGTACAGCAATCAAAGGTCACCTTTCAATGGTT

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 47
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 49
--gtctgcctcccttg-atagctcttcaacttttttcttgttttttt----------gaac---gtccatcatgtatcatctg-tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT
   | |  ||   ||| ||||   | |  ||| ||| || |||||             |||     |||   | |||  |||  | || | ||||||||||||||||||||| || ||  ||||||| ||||||||  ||||||||||||| |||||||| ||  | |||||||||||||| ||||||||||||
gtatataactttgttggatagagttactgcttcttttttttttttccttataaaataaaactagaaccactttttattttctaatgttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTTCTGCATGAACTTGTCAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTT

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 47
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 48
----gtctgcctcccttg-atagctcttcaacttttttcttgttt------------ttttgaacgtccatcatgtatcatctgtattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT
     | |  ||   ||| ||||   | | ||| |  | || ||              |   | |    ||  | |||  | |   || | ||||||||||||||||||||| || ||  ||||||| ||||||||  ||||||||||||| |||||||| ||  | |||||||||||||| ||||||||||||
gtatatataactttgttggatagagttactactctcctttttttaaaaaaaaaaaaactcgaatcacttattttctattgttttatttgtatagGGCTGGTGCTGATGACAAACCTTTACGAATGGTAAAAACTGTACTGCATGAACTTGTCAAGCTTCGTGGTGCAGCAATAAAGGGTCATCTTTCAATGGTT

upper sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 47
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 18
-------------------------------------------gtctgcctcccttgatagctcttcaacttttttcttgtttttttgaacgtccatcatgtatcatctgtatt-----------ctgtagG-GCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT
                                            | ||  |     |  |     |  | |||| || |   ||  | || || | || | |  |   |  | |           |  || | ||||| ||||||||||| |||||  | ||||| ||||||||  | ||||||||||| |||||||| ||||| |||||||||||||||||||| ||||||
gtatcccttgtgtaatcaagttccgaaaaatttcaggatttttctttgttttttaggcaatgcagttgatttttatcattagttgcttaatgttcttcttttggctgttacaatgaaatgaactaccataagAGCTGGAGCTGATGACAAACCATTACGCATGGTTAAAACTGTTCTACATGAACTTGTTAAGCTTCGCGGAACTGCAATAAAGGGTCACCTTTCTATGGTT

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|93014606|gb|EB640126.1|EB640126
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|32834298|gb|CD973976.1|CD973976
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|67021414|gb|CO450163.1|CO450163
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|37424588|gb|CF650027.1|CF650027
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|32838771|gb|CD978452.1|CD978452
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|67015335|gb|CO444084.1|CO444084
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|32834018|gb|CD973696.1|CD973696
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
EST: gi|71317537|gb|DR795494.1|DR795494
EST:     AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAG                         GGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA
genomic: AGCATCCATATTTATTTACAAGAACTTGGGATGGAAGAAATACGGAGAAGgtctgcctcc ... tattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaacttttttcttgtttttttgaacgtccatcatgtatcatctgtattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT
     ttttttcttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcctcccttgatagctcttcaacttttttcttgtttttttgaacgtccatcatgtatcatctgtattctgtagGGCTGGTGCTGATGACAAGCCATTGAGAATGGTCAAAACTGTCTTGCATGAACTTGTGAAGCTTCGGGGAACGGCAATAAAGGGTCACCTTTCAATGGTT

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