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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgttctttggagttcttttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag

Basic information

species Zea mays
transcript GRMZM2G088212_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g51150.1 (Oryza sativa), 5'ss of exon 4
TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgttctttggagttct---tttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag
||| ||||||||| |||||||||||||||||||||||||||||||  ||||||| |||||||| ||||| | |||||| |||||||||||||| ||||||||||| |||   |     |||     | |  ||  ||||| ||  ||| |||    |||||||||  ||||  |  |   | |||| | |    |  | | ||                            
TGGCCCAAACTATTTGATGCTTCCTGTGAATGCACCAAAATGTGCATACCACAACAACCACCACGATGGCTCCATGAATTTCATGCACAGGGATGAAGAGgtactgtgtgtatatactttcagagatacatctcctgcattcagttgttgtg----atgcatctt-tctgtttttgtccattacatattgtttcttccagtcaac--------------------------

upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 3
lower sequence: EDP00871 (Chlamydomonas reinhardtii), 5'ss of exon 11
TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgt--actatgttctttggagttcttttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtc--gtcataagtaacatgtgggagttct-ctggcacttatacctatcctctctgtttccttag----------------------------------
                    | || ||||| || ||        |||||||||| |||||||| || || |||||||||||||||||| | ||||| ||  |  ||||  | |   | || |         |   ||  |   | | ||||  | | |        ||||     |   | |  | ||  ||    |  |||     | |       || ||      ||  |                                  
--------------------TGCCGGTGAACGCGCCGCGCGCCCCCCACCACAACAACCACCACGAGGGCTTCATGAACTTCATGCACCGCGACGAGGAAATCAACTACTTCCCCAGCAGgtggggcgggatcaggcg-gtcggcggggtggggcaggtggtgcgactgtgtgaccgacattggcctgcaggctcccggctgatgtctgtgtgcgagctttcgcaagtctcggtatccgaccaagcgcccgcccacgcgatgcacag

upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ36549 (Selaginella moellendorffii), 5'ss of exon 5
TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgttctttggagttcttttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag
 || || || ||  || ||||||||| ||| || || || ||||| || ||||| ||||| || || || |||||||||||||  ||||||||||||||||||  |    ||||   | |  |     || |  | ||    ||  |                                                                                 
GGGGCCGAATTACTTGCTGCTTCCTGCGAACGCTCCCAAGTGTGCTCATCACAACAACCATCACGAGGGATTCATGAACTTCACCCACAGGGACGAAGAGgtatgacaagctttt--gcttatacgttctatatcctgtgtttgcag---------------------------------------------------------------------------------

upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ36547 (Selaginella moellendorffii), 5'ss of exon 2
---TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgttctttggagttcttttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag
     | || |||||| || ||||||||| |||||| || || ||||| || |           || || || |||||||||||||  ||||||||||||||||||  |    |   |   ||  |||  | || |  || |  ||||  || ||                                                                            
GCTGAGGCCGAACTATTTGCTGCTTCCTGCGAATGCTCCCAAGTGTGCTCATC----------TCACGAGGGATTCATGAACTTCACCCACAGGGACGAAGAGgtatgacaagcaacgctcttgcttttacgttctatattct-gtgtt-tgcag----------------------------------------------------------------------------

upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ33688 (Selaginella moellendorffii), 5'ss of exon 4
TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgttctttggagttcttttccccttttgcat-gcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag
||| || |||||||| ||||| ||||  |||||||| || || || || |||||||| || || || || || |||||||||||||||||||| || ||||||   || |    ||| |  | | |   |||| | | |   | |   | |   |||  |  |||  ||  |           | |  || || |||  |   |   | |   || ||     |     
TGGACCGAACTATCTCATGCTGCCTGCAAATGCACCCAAGTGCGCACATCACAATAATCATCACGAAGGCTTTATGAACTTCATGCACAGGGATGAGGAGgtatggtggt----ggaatgttctccagttttttctttgtttgagctttttttaatgatttgtactcgttct--------gtctttttgatttttctaaccactcgtcgtgaactgtcaaacacag---

upper sequence: GRMZM2G088212_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ37039 (Selaginella moellendorffii), 5'ss of exon 4
TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt------ctttggagttcttttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag
||| || |||||||| ||||| ||||  |||||||| || || || || |||||||| || || || || || |||||||||||||||||||| || ||||||   || |       | |  |||| |||     |||    |     |   |  | | |  | |  |  || | |   |   ||||   | |  ||   ||| ||   | |                      
TGGACCGAACTATCTCATGCTGCCTGCAAATGCACCCAAGTGCGCACATCACAATAATCATCACGAAGGCTTTATGAACTTCATGCACAGGGATGAGGAGgtatggtggtggaatgttctccagttttttctttgtttgagctttttttaatgatttgtactcgttctgtcttttgatttttctaaccactcgtcgtgaactgtcaaacacag---------------------

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|28569014|gb|CB280889.1|CB280889
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTC
EST: gi|211372725|gb|FK987862.1|FK987862
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCC
EST: gi|31355364|gb|CD439721.1|CD439721
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|51592848|gb|CV071994.1|CV071994
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACCTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|8367869|gb|BE050814.1|BE050814
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|6563780|gb|AW231312.1|AW231312
EST:     AACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: AACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|213172790|gb|FM182986.1|FM182986
EST:     ACAACAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|83278461|gb|DV942469.1|DV942469
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|51592345|gb|CV071491.1|CV071491
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|44681843|gb|CK786891.1|CK786891
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTT
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTT
EST: gi|33770839|gb|CF273133.1|CF273133
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCC
EST: gi|44681821|gb|CK786869.1|CK786869
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAA
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCC-TTCGAGGTTTGATCCCGCCCGTCACGCGGAGAA
EST: gi|45567401|gb|CK985553.1|CK985553
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|60348828|gb|DN215801.1|DN215801
EST:     TGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: TGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|60357381|gb|DN224354.1|DN224354
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|8930216|gb|BE224980.1|BE224980
EST:     ACAACAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|31350569|gb|CD434926.1|CD434926
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGTATAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|8366919|gb|BE049927.1|BE049927
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCAGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|31250271|gb|CD219295.1|CD219295
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGA
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGA
EST: gi|13237225|gb|BG355239.1|BG355239
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|83279341|gb|DV943349.1|DV943349
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|60342963|gb|DN209936.1|DN209936
EST:     CACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: CACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
EST: gi|38502631|gb|CF972491.1|CF972491
EST:     ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAG                         GTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC
genomic: ACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgtt ... gtttccttagGTGAACTACTTCCCTTCGAGGTTTGATCCCGCCCGTCACGCGGAGAAGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCCAAACTATCTGATGCTTCCTGTGAATGCACCAAAATGTGCCCACCACAATAACCACCATGATGGGTTCATGAACTTCATGCACAGGGACGAAGAGgtactatgttctttggagttcttttccccttttgcatgcaagtgtggtgtaggatgcatcttacctgtcgtcataagtaacatgtgggagttctctggcacttatacctatcctctctgtttccttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA