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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcatctgtaatcacattgtcttgctgtgaatccaattctgaattggaaagttttacaccaatctcacaacttggacaatgtacattttctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCAAGCGATGATGGAGTTAGGAGCAACATTATGTAGCAAGACAAAGCCTGGT

Basic information

species Zea mays
transcript GRMZM2G425986_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G425986_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g10850.1 (Oryza sativa), 3'ss of exon 4
gtttcatctgtaatcacattg-tcttgctgtgaatccaattctgaattggaaagttttacaccaatctcacaacttggacaatgtacattttctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCAAGCGATGATGGAGTTAGGAGCAACATTATGTAGCAAGACAAAGCCTGGT
 |   | |  |   || |  | |||| |||       |  | |  | || ||         | |||   |   | |    |    |  |  |  || | ||| | |||   ||| || ||||||||||||  || |||||||||||||||||||| ||||||||  ||||||||||| | || |||||||| |||||||||
-tcgtaccactttccatacagctctttctgaattagaagctttatactgaaatagaacttccaaattgtatggcctttgaacatcatttccttgatcacagGCAGCTCACTGGTGAACTGGTTGACCCTTCAAGGCCAGGAGACTTCAACCAAGCAATGATGGAACTAGGAGCAACACTCTGCAGCAAGACGAAGCCTGGT
















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|76932963|gb|DV173258.1|DV173258
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|71323508|gb|DR798415.1|DR798415
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|71299540|gb|DR785778.1|DR785778
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|91874808|gb|EB404765.1|EB404765
EST:     ACACCATTGCTGACAACCCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCCACCA
genomic: ACACCATTGCTGACAACCC-AAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|71441857|gb|DR822907.1|DR822907
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|78090907|gb|DV519281.1|DV519281
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCCTCGTAAGTCAA-TGGTTGACCCTTTGAGACCAGGAGACTTCACCC
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACC-TCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACC
EST: gi|76926659|gb|DV170957.1|DV170957
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|71323967|gb|DR798666.1|DR798666
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|78103468|gb|DV521896.1|DV521896
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|74245470|gb|DT653384.1|DT653384
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|71446168|gb|DR827218.1|DR827218
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
EST: gi|6865197|gb|AW360547.1|AW360547
EST:     TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTG                         GGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA
genomic: TACACCATTGCTGACAACCCAAAGGAATCCTCAACAGTGAAGAGATTCTGgtagactgca ... tctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaaagttttacaccaatctcacaacttggacaatgtacattttctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCAAGCGATGATGGAGTTAGGAGCAACATTATGTAGCAAGACAAAGCCTGGT
                  atctcac  putative branch site (score: 3)
                                        cattttct  putative PPT
                                      tacattttctataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcatctgtaatcacattgtcttgctgtgaatccaattctgaattggaaagttttacaccaatctcacaacttggacaatgtacattttctataatagGGACCTCGTAGGTCAAATGGTTGACCCTTTGAGACCAGGAGACTTCAACCAAGCGATGATGGAGTTAGGAGCAACATTATGTAGCAAGACAAAGCCTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA