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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttagcatccattctttcataacttagactatgaataactcttgttgcttcatgtcattgactggaatatacgcaactttgccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTTTGGGCTTGGCGCAGAG

Basic information

species Glycine max
transcript GLYMA01G24530.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G24530.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 17
-tattttagcatccattctttcataacttagactatgaataactcttgttgcttcatgtcattgactggaatatacgcaactttgccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTTTGGGCTTGGCGCAGAG
 | ||| |  |       || || ||||   | ||||  |  | ||| ||  | |||  | || | |  |||  | |  | | | |  |   |   ||||||||||| |||||||| |||||||| |||||||| |||||||| || |||||||| || || || |||
gtgtttaactaatttcctttgcacaact---attatgtttgccgctt-ttagtacatacc-ttaatt--aatgga-gttattcttctataaattgcaacagTGCTGCGGTATTCCATAATGCAAGCACACGGTTCTGTGATGGGGCTCGCTTTGGTCTAGGTGCTGAG

upper sequence: GLYMA01G24530.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 17
----tattttagcatccattctttcataacttagactatgaataactcttgttgcttcatgtcattgactggaatatacgcaactttgccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTTTGGGCTTGGCGCAGAG
     ||   |   ||  |   ||  |    ||   ||||   || | |||    |   |||  || ||    | ||  |   | ||  ||    |   ||||||||||| || ||||| ||||||||||| || ||||||||||||||||| ||||| ||||| ||||||
tacaaatgcaatggtctgtaaattgtttgagtaatttatgctaaattgttgcacatatttgt-gttaaccttgaaatgtggctcattatct---atctcaacagTGCTGCAGTTTTCCATAATGCAAGTACCCGATTTTGTGATGGAGCACGTTTTGGACTTGGTGCAGAG
















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|254314111|gb|GR831740.1|GR831740
EST:     GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGACAG                         TGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT
genomic: GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGACAGgtatgtctag ... gtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT
EST: gi|151398324|gb|EV268195.1|EV268195
EST:     GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGGCAG                         TGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT
genomic: GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGACAGgtatgtctag ... gtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT
EST: gi|6724716|gb|AW309049.1|AW309049
EST:     GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGACAG                         TGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT
genomic: GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGACAGgtatgtctag ... gtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGC-T
EST: gi|11117946|gb|BF219539.1|BF219539
EST:     GTTACAGAAGATAGTGAAGTTGCTGAGACTTNNNNNAGTCAAGTTGACAG                         TGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT
genomic: GTTACAGAAGATAGTGAAGTTGCTGAGACTTTCTTAAGTCAAGTTGACAGgtatgtctag ... gtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgcttcatgtcattgactggaatatacgcaactttgccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTTTGGGCTTGGCGCAGAG
             cattgac  putative branch site (score: 3)
                       aatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttagcatccattctttcataacttagactatgaataactcttgttgcttcatgtcattgactggaatatacgcaactttgccttgtgtacaaacagTGCTGCTGTATTCCACAATGCAAGTACACGGTTTTGTGATGGAGCACGCTTTGGGCTTGGCGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - -gcatcca
- - - - - - - - - - - - - - - -ctatgaa
- - - - - - - - - - - - - - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgactg