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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcagtctgatcttgttaaaccattttgctagctacctatcatttagctgaaatgctctatcataccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG

Basic information

species Zea mays
transcript GRMZM2G097226_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 3'ss of exon 8
gtatgtcagtctgatcttgttaaaccattttgctagctacctatcatttagctgaaatgctc-tatcataccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG
|||||  |   |||||||||||  | ||    ||  ||| |  ||||||  |  | |||||  |||  ||   | ||||| ||||||||||| |||||  ||||||||||||||||||||||||||||    || || ||||||||||| |||
gtatgg-aacatgatcttgttatgctat---actgactagccgtcatttccccaagatgctgatatactattttctgcagCTATGGAGAATCATTCCCTATTTCTGCTGAAGTGCTTGATTCTAGTTTCGCTCTGCCAATTGGCAAAGCAAAG
















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|32802035|gb|CD954271.1|CD954271
EST:     CCTGATCCTGTTATTTTCTTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: CCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|32829636|gb|CD969314.1|CD969314
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|211317947|gb|FL318710.1|FL318710
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|32940983|gb|CF045802.1|CF045802
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAAT
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAAT
EST: gi|32829111|gb|CD968789.1|CD968789
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|60343110|gb|DN210083.1|DN210083
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|211088145|gb|FL307530.1|FL307530
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
EST: gi|91057168|gb|EB167586.1|EB167586
EST:     GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCT                         TTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG
genomic: GCTGCTATCAGGGACCCTGATCCTGTTATTTTCCTGGAAAATGAATTGCTgtatgtcagt ... ccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattttgctagctacctatcatttagctgaaatgctctatcataccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG
                 tatcattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcagtctgatcttgttaaaccattttgctagctacctatcatttagctgaaatgctctatcataccatttgcagTTATGGAGAATCTTTCCCAGTTTCTGCTGAAGTGCTTGATTCTAGTTTTTGCCTACCGATTGGCAAAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG