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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccattgcaatcgaatacgattactatgtacatagttcaagttgtgttgctactataacatatgcatagtaattgctatatatgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCAGTGATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCA

Basic information

species Glycine max
transcript GLYMA12G01680.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G01680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0039g01410.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------gtacccattgcaatcgaatacgattactatgtacatagttcaagttgtgttgctactataacatatg-----catagtaattgctatatatgttat-gtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCAGTGATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCA
| | | | || | |||| | | || || | || | |||| || | || | | || ||||| | |||| |||||| | | |||||||||| | |||||| ||||||||||| |||||||||||||| || ||||| | || ||| ||| ||||| || ||||
gtacctaatctgactattaatgcatgtaatgtgtgctaaaaaaaaaaacacacacacacaccttgaatgtgactgctgtctgctcaggtttggacttatcccagtgtatggaccatgaactgctttttatccattatgtatgttaaacacaagaagttcccaattcgttattgcagGATATCAAGGCCGCAGATTGGTCTGAGTATGTTGCACCCTTTTGGCCAGCAGTGATACGCTCTGCTTTGACGTTCAAGGGCTTCATATCACTGTTACGCA
















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|120531233|gb|EH259366.1|EH259366
EST:     GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAG                         GACATCACGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGGCCGCA
genomic: GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAGgtacccattg ... tgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
EST: gi|151406224|gb|EV276039.1|EV276039
EST:     GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAG                         ----TCA-G--A-A-GATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
genomic: GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAGgtacccattg ... tgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
EST: gi|58023365|gb|CX710106.1|CX710106
EST:     GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAG                         GACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
genomic: GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAGgtacccattg ... tgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
EST: gi|57575258|gb|CX548233.1|CX548233
EST:     GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAG                         GACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
genomic: GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAGgtacccattg ... tgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
EST: gi|193380261|gb|FK348695.1|FK348695
EST:     GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAG                         GACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
genomic: GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAGgtacccattg ... tgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCA
EST: gi|192319801|gb|FK013801.1|FK013801
EST:     GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAG                         -ACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCG
genomic: GGTGCTCAGCTTCTGATTATGTCAAATTGCTCCAATCCCTGTCACTTCAGgtacccattg ... tgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttgtgttgctactataacatatgcatagtaattgctatatatgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCAGTGATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCA
               ctataac  putative branch site (score: 3)
 tatatatgttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccattgcaatcgaatacgattactatgtacatagttcaagttgtgttgctactataacatatgcatagtaattgctatatatgttatgtagGACATCAAGTCAGAAGATTGGTCTCGCTTTGTTGCTCCCTTTTGGCCCGCAGTGATACGCTCCGCGTTGACATGGAATGGCCTCACTTCACTCTTGCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA