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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctgcctgtctccattgtcgttatgtaagtttactcatgtaattagcatagatatgttttcacttcatttgatctgctcatatcgttgatgatggtaaaaaaaacattgaaataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG

Basic information

species Zea mays
transcript GRMZM2G005859_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005859_T02 (Zea mays), 3'ss of exon 4
lower sequence: 13114.m00108 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------gtatgtgctgcctgtctccattgtcgttatgtaagtttactcatgtaattagcatagatatgttttcacttcatttgatctgctcatatcgttgatgatggtaaaaaaaacattgaaataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG
                                                                      |    | |||   |   ||||  || |  | | | |||   ||||| | |   |   |  ||    | | |||  |||  || |     | | | || || |   || ||      |||||||||| || ||||| |||||||| |||||| |||| ||||| ||||| || ||||||||||||||||| |||
gtatttgcttcatgtccattatctatttctgcttaattagatttctttcgaagtcctattacagattacttaccttacctacatggcttgtaattgtaaatggt-actacagtaatgatctgtgcagtaattggcatgcgttt--tcttttccttattctcacgttg-tagagcgaatataactgaaattgtagGGTGCGTTGGCTGATATTTTTCTGAGAGGCACAGAGCTCATGAAAGACGCTCGAGGGATTGCATCCCTG
















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|211010141|gb|FL113888.1|FL113888
EST:     GGCTGCTAGCTCAATTGGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG                         GGAGCACTGGCCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGC
genomic: GGCTGCTAGCTCAATTGG-CGAGGAGCTGTTCTACCGCGCCGCCATTCAGgtatgtgctg ... ataattgtagGGAGCATTGGCC-GATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGC
EST: gi|71445181|gb|DR826231.1|DR826231
EST:     TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG                         GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCT
genomic: TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAGgtatgtgctg ... ataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCT
EST: gi|5525259|gb|AI861098.1|AI861098
EST:     TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG                         GGAGCATTGGCCGATATTTTC
genomic: TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAGgtatgtgctg ... ataattgtagGGAGCATTGGCCGATATTTTC
EST: gi|78022617|gb|DV491004.1|DV491004
EST:     TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG                         GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCT
genomic: TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAGgtatgtgctg ... ataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCT
EST: gi|76290855|gb|DV030423.1|DV030423
EST:     TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG                         GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCT
genomic: TGGCTGCTAGCTCAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAGgtatgtgctg ... ataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCT
EST: gi|78091085|gb|DV519459.1|DV519459
EST:     GGCTGCTAGCTNCA-TTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAG                         GGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCT
genomic: GGCTGCTAGCT-CAATTGGCGAGGAGCTGTTCTACCGCGCCGCCATTCAGgtatgtgctg ... ataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgatctgctcatatcgttgatgatggtaaaaaaaacattgaaataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG
                 cgttgat  putative branch site (score: 5)
                             taaaaaaaacattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgctgcctgtctccattgtcgttatgtaagtttactcatgtaattagcatagatatgttttcacttcatttgatctgctcatatcgttgatgatggtaaaaaaaacattgaaataattgtagGGAGCATTGGCCGATATTTTCCTGAGAAGCACGGAGCTAATGAAGGATGCTCGAGGGATTGCATCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG