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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcatattgctggttctcaaatttgatgttctgttaaacaccatttgtcagtagtgaccttttgcttttttttttcctttgtaataataatcatttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTCTTCCCAATAAGACTCTTAATGTCCGTGTGCAAGAAGAAATCATCTTATA

Basic information

species Glycine max
transcript GLYMA19G06900.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G06900.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g11050.1 (Oryza sativa), 3'ss of exon 14
----atttcatattgc---tggttctcaaatttgatgttctgttaa-acaccatttgtcagtagt---gaccttttgcttttttttttcctttgtaataataatca--tttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTCTTCCCAATAAGACTCTTAATGTCCGTGTGCAAGAAGAAATCATCTTATA
        ||   |||   |||    | |     || || || ||| |  |  | ||   || |    |  | | || ||   ||    | || |    ||    |  |  ||||||||| ||    |||||||||||||| || ||  ||||| ||||||| || |||||||| ||||| |||||| |||||||||| || ||||| |||| 
gtaagacccagtctgcacatggcctcccacaagaatcttgtgataatatgctttgtgcgtgtgggttagttcctatgattgagttgacacattatctctatttctaaatgcagGTGAAGCCGTTGATGTTGAAGATGAAGTGGTTGTAGTTAACAGCATTGTGCTCCCCAATAAAACTCTCAATGTCAGTGTGCAAGAGGAGATCATATTATG

upper sequence: GLYMA19G06900.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G178254_T01 (Zea mays), 3'ss of exon 14
atttcatattgctggttctcaaatttgatgttctgttaaacaccatttgtcagtagtgaccttttgctttt-ttttttcctttgtaataataatc--atttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTCTTCCCAATAAGACTCTTAATGTCCGTGTGCAAGAAGAAATCATCTTATA
            |    | |||||| |||| | |    ||||  |||    | || |    |  |  |||  ||| |    |||  ||  || |   |   ||||||||| ||    ||||||||||||||||| ||  ||||| |||| || || || ||||| ||||| |||||| |||| ||||| || |||||| ||||
-----------gtaagacccaaatt-gatgatttac--aacagtattc-caaataattttgtgataatttcgtttctggaattgacatcctattttaacacagGTGAAGCCGTTGATGTTGAAGATGAAGTAGTTGTAGTTAACAGCATCGTGCTCCCAAATAAAACTCTCAATGTCAGTGTCCAAGAGGAGATCATCCTATA
















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|6566807|gb|AW234439.1|AW234439
EST:     GCTGATGGTAACTATGATTCAAAACTTGGCACAACCATCTTAG                         GTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTATAACTGCATTGTTC
genomic: GCTGATGGTAACTATGATTCAAAACTTGGCACAACCATCTTAGgtacatattc ... aatcatttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTC
EST: gi|193567058|gb|FK523311.1|FK523311
EST:     GCTGATGGTAACTATGATTCAAAACTTGGCACAACCATCTTAG                         GTGAAGCTGTAACGG
genomic: GCTGATGGTAACTATGATTCAAAACTTGGCACAACCATCTTAGgtacatattc ... aatcatttagGTGAAGCTGTAACGG
EST: gi|193452016|gb|FK418450.1|FK418450
EST:     GATTCAAAACTTGGCACAACCATCTTAG                         GTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATCGTTC
genomic: GATTCAAAACTTGGCACAACCATCTTAGgtacatattc ... aatcatttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcagtagtgaccttttgcttttttttttcctttgtaataataatcatttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTCTTCCCAATAAGACTCTTAATGTCCGTGTGCAAGAAGAAATCATCTTATA
                      ttttttttttcctttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcatattgctggttctcaaatttgatgttctgttaaacaccatttgtcagtagtgaccttttgcttttttttttcctttgtaataataatcatttagGTGAAGCTGTAACGGTTGAAGATGAAGTAGTAGTGTTTAACTGCATTGTTCTTCCCAATAAGACTCTTAATGTCCGTGTGCAAGAAGAAATCATCTTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - -tgctggt
- - - - - - - - - - - - -tgatgtt
- - - - - - - - - - - - - - - - - - - -acaccat