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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtacgggcggtgtatatatttttgttttatatcgttgtttggatcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT

Basic information

species Zea mays
transcript GRMZM2G127949_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127949_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g63770.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------tctgtacgggcggtgtatatatttttgttttatatcgttgtttggatcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCA--AGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT
                                                    | | ||  ||||| ||   | ||  || | | | | |||   |  || |||  ||| || |    |  || ||  | ||  ||       |   ||||||| | ||  |  || | ||| | | | |||  | | || |||||||||||  ||||||| |||||||||| ||| |||||||||||||||| |||||||||| 
gttggtgctcttcttcttcttcttcttgctgctgcagctggtggtgttgttttttttattggcggggtcggt-ttcctgctctgttttgttaagtc-atattgtgctgtcctggatcttgatccg-acgtccgtccgtacgcactcacgcagCTGACGACGG-GGAAGGGCGGCGTGGTCAGCATGGTGCCGCGCGAGCAGGCGGAGGAGGCCATCGTGGCTGACAGCAACGGCAAGGAGGAGGAGGTCGGGG-
















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|71767266|gb|DR965203.1|DR965203
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAG                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|76293069|gb|DV032637.1|DV032637
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAG                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|76012875|gb|DT940045.1|DT940045
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAG                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|19351481|gb|BM896013.1|BM896013
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAG                         CGTGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|91874014|gb|EB403971.1|EB403971
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTC----                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|91055745|gb|EB166163.1|EB166163
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAG                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|78122313|gb|DV540697.1|DV540697
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAG                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
EST: gi|71327831|gb|DR800545.1|DR800545
EST:     GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTC----                         CGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG
genomic: GCCAACCGCGCGGCGCGGCCACCACGCTAGGCCCCTCGCCCTCCTCGTAGgtgaacagag ... aacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT
              ggctgat  putative branch site (score: 4)
                   atgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtacgggcggtgtatatatttttgttttatatcgttgtttggatcttgatctggccggctgatgaatacgtgcttctctctccgacgaacgacgcagCGGGCGGAGACGGGAAGGCCGTGCGCTCAAGGATGGCGCGCGAGCAGCTGGAGGAGTCCATCGTGGCCGACGGCAACGGCAAGGAGGAAGAGGTCGGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG