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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggaatatatataatttgtggtgcacgcagttttatttgaactgcatgcagagaatcatggatcctgttccgggtgacgggtgttgctcatgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCGGAATGGTGCGTCCCATGCGCCAAGTTCACTCCAAAACTGATTTCTGTTT

Basic information

species Glycine max
transcript GLYMA06G02380.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02380.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g01030.t01 (Vitis vinifera), 3'ss of exon 2
taggaatatatataatttgtggtgcacgcagttttatttgaactgcatgcagagaatcatggatcct-gttccgggtgacgggtgttgctcatgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCGGAATGGTGCGTCCCATGCGCCAAGTTCACTCCAAAACTGATTTCTGTTT
||    | |||||  ||| |  |    |   | | | |   | ||||||   | | |  || ||  | |    || | |  ||||     | | |   ||||| ||| || |||   || | || || ||||| |||||||||||||||||  |||||||  | ||| |||  ||||||||||| |||||||||||  | |
tatttttttatattttttttattctttggcatgtgaatatgaatgcatg-gtaaattattgcatagtagggatggctcattggtgggtgacttatgtgcagGTGCCTATTTCTTCTTTAATAGGCAAGACAATCGGACTCTACTTCTCAGCTCAATGGTGTCTTCCAGGCGTGAAGTTCACTCCCAAACTGATTTCCATCT
















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|11273893|gb|BF324282.1|BF324282
EST:     ACCACCACAGA--CTATGTTTTGAGTCACACTCACACGGGACTCAAAAAG                         GTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
genomic: ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAGgtaaatggct ... atgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
EST: gi|19270436|gb|BM886692.1|BM886692
EST:     ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAG                         GTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
genomic: ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAGgtaaatggct ... atgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
EST: gi|11274696|gb|BF325031.1|BF325031
EST:     ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAG                         GTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
genomic: ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAGgtaaatggct ... atgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
EST: gi|19270531|gb|BM886787.1|BM886787
EST:     ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAG                         GTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
genomic: ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAGgtaaatggct ... atgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
EST: gi|151403360|gb|EV273170.1|EV273170
EST:     ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAG                         GTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
genomic: ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAGgtaaatggct ... atgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCG
EST: gi|22541185|gb|BU091028.1|BU091028
EST:     ACCACCATAGAGACTATGGTTTGAGTCACACTCACACCGGACTCAAAAAG                         GTACCTTGT-GCTTGGCTAGTGGGTTAAACAATTGGACTCTACTTCTCAGC
genomic: ACCACCATAGAGACTATGTTTTGAGTCACACTCACACGGGACTCAAAAAGgtaaatggct ... atgtacacagGTACCT-GTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggaatatatataatttgtggtgcacgcagttttatttgaactgcatgcagagaatcatggatcctgttccgggtgacgggtgttgctcatgtacacagGTACCTGTTGCTTGGCTAGTGGGTAAAACAATTGGACTCTACTTCTCAGCGGAATGGTGCGTCCCATGCGCCAAGTTCACTCCAAAACTGATTTCTGTTT

- - - - - - - - -tgtggtg
- - - - - - - - - - - - cacgcag
- - - - - - - - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtgtt