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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacaatctctgccagtgacagcttcctgattcgaacctgacctgacaatgtcaccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT

Basic information

species Zea mays
transcript GRMZM2G024389_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024389_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g63360.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------gtaaacaatc-tctgccagtgacagcttcctgattcgaacctgacctgacaatgtcaccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT
                                                        | |   || |    || | ||| | |    ||    |       || ||   |||  |||||||||||| | || |||||||| ||||| ||||||||||| ||||||||||| ||||||||||| | ||| ||||| ||||||| |||||  | |   ||  
gtacagattcctccaaattaaaatgctccgcatctagcttcattactaccgagtacatatgttcgttcctcacttacaacattacaatattgatgatcaatgtcatcctcatgaatcagGATGACATTGGTGACAAATCAGTTTTTATGTTCAACGCCCTCCCTGAAGAAGAAAAGAAGGCCTTGATACAGAAGCTCGAGATGCAAACTGAGACCGATG

upper sequence: GRMZM2G024389_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G39400.2 (Glycine max), 3'ss of exon 2
-----------------------gtaaacaatctctgccagtgacagcttcctgattcgaacctg--acctgacaatgtcaccaatc---agGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT
                        |   |  |   | | | |      |  ||   | || | ||  ||       |  || ||| |   |||||||| |||| ||||| |||||||||||||||||  |||| ||||  || || | ||| || | | |  ||||| | ||   ||||||    ||  | |
gtatatttacttttacttttctctttttctgttcatacaattagtttatatcttcattgatcttgggactcatgcttaacatcaaactcaagGATGACATCGGTGACAAGTCTGTTTTCATGTTCAATTCTCTTCCTGGTGACGAGAGGAAAGCCTTGCTTGAGAAATTAGAACAGCAAAAAATTCAGAATT

upper sequence: GRMZM2G024389_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0150g00130.t01 (Vitis vinifera), 3'ss of exon 4
-------------------gtaaacaatctctgcc-agtgacagcttcctgat-----tcgaacctgac---ctgacaatg-----tcaccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT
                   |     | |||||  | ||| ||  |||| || |     ||| || | ||   ||||||        | ||     |||||||| | || ||||||||||| ||||||||||| || ||  | ||||||||||||| ||||| |||  |||| || |||   |||||     |  |  
gtataaaatcccaatcaatgctggtagtctctatctagtaac--cttcatggtatttatcggacatcacacactgacatctctcctttactttcaagGATGACATTGGCGACAAATCTGTATTCATGTTCAATGCCCTTGCGGAAGAGGAAAAGATGGCTTTGATTGAGAAGCTTGAGCAACAAAAATTAAAGAACC

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|32842411|gb|CD982092.1|CD982092
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTTGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCCGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|71445141|gb|DR826191.1|DR826191
EST:     TGCTTCTTTTCACAATTTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|5777299|gb|AI974918.1|AI974918
EST:     TGCTTCTTTTCCCAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|32842847|gb|CD982528.1|CD982528
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTTGGAGACAAATCTGTTT
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTT
EST: gi|113703906|gb|EE681410.1|EE681410
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|149096204|gb|EE181903.2|EE181903
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|6952409|gb|AW424477.1|AW424477
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|32842556|gb|CD982237.1|CD982237
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTTGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCCGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
EST: gi|18179095|gb|BM380305.1|BM380305
EST:     TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAG                         GATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG
genomic: TGCTTCTTTTCACAATCTTCGCCGCTAGAAAATTCCAGCAGCCCATCAAGgtaaacaatc ... caccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgccagtgacagcttcctgattcgaacctgacctgacaatgtcaccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT
                                 acctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacaatctctgccagtgacagcttcctgattcgaacctgacctgacaatgtcaccaatcagGATGACGTCGGAGACAAATCTGTTTTCATGTTCAACGCTCTCCCTGAAGAGGAAAAGAAGGCTTGGATCCAGAAACTCGAGAGGCAAAAGGGGCAAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA