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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA

Basic information

species Zea mays
transcript GRMZM2G127453_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g56890.3 (Oryza sativa), 3'ss of exon 1
gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA
    || ||  ||  |  | | | | | || || | |||  || || |  || |||||||     | || |   ||||| |||||||||||||||||| || |||||| |||| ||||||||  | | |||||| |||||||||||||||||||||||||| ||||| ||||| ||  ||||  
----gtgcgttcccttttctcggttcggtttggttggtg--ggggaaggggg-taattctaattctgggct---tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
















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|211045913|gb|FK963041.1|FK963041
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211042956|gb|FK963034.1|FK963034
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211042950|gb|FK963028.1|FK963028
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211045917|gb|FK963045.1|FK963045
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211167599|gb|FL258648.1|FL258648
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211042953|gb|FK963031.1|FK963031
EST:     GCGTTTCCACGCAGGAAGACTCCGNCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211115674|gb|FL110115.1|FL110115
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211045915|gb|FK963043.1|FK963043
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATCGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGARGCA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCA
EST: gi|211115672|gb|FL110113.1|FL110113
EST:     GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAG                         CATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGA
genomic: GCGTTTCCACGCAGGAAGACTCCGCCGCCTACGCCCTCGCCATCATGAAGgtacgtacgc ... tgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA
                     ggctaat  putative branch site (score: 3)
                                            ttgctcc  putative PPT
                        taattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG