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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatgagccgtttagtggtttatgcttgccttttttacctgatctgtgttcggtcaaagttgctcgttcgtcctgatctgatcttgtttcactgtgtgacaattttgagtacggtgtgtgttttggttgactttgggtttggattaatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA

Basic information

species Glycine max
transcript GLYMA03G38340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 2
gtattatgagccgtttagtggtttatgcttgccttttttacctgatctgtgttcggtcaaagttgctcgttcgtcctgatctgatcttgtttcactgtgtgacaattttgagtacggtgtgtgttttggttgactttgggtttggattaatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                                |      | |||| |  ||  ||| ||   || || ||   |  |  | |||  |  |||    |   |||  | |||    | || |||   ||    |  ||   ||||||||||||||    ||||||||||| |||||||| ||||| ||||| |||||  ||||||| ||| | |||| ||| |||||| |  || ||
------------------------------------------------gacacatgacaaaatatct--ttcctcgaaatttggtc--atcgctttttgtacctctttcttttcatgtgactatttca--taacattgctatt----tgttcctacagGTTGTTGTTAACAGTGAAATGATTGAGTACTATGACATTTCTGGTTGTTATATATTGAGGCCATGGGCGATGGAAATCTGGGAGCTACTGAAA

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G62120.2 (Arabidopsis thaliana), 3'ss of exon 2
gtattatgagccgtttagtggtttatgcttgccttttttacctgatctgtgttcggtcaaagttgctcgttcgtcctgatctgatcttgtttcactgtgtgacaattttgagtacggtgtgtgttttggttgactttgggtttggatta-atctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                                              ||| |  |  || |     |||   ||||||    |       ||||  || |   |   ||| |   |||| |  | |||   |||  |||| |  | | |||| ||    || |||||||| ||||| ||||| || || || ||||||||  |||| ||||||||||| || |||||||| ||||||
------------------------------------------------------------gtttgtttatatgttcaacgatgag--tgtttccacattc-----ttttttgtcccaagctggttata--tgacatctgcttttctttatgtctgtctagGT-TTGTAAACAA-GATATGATTGAGTACTACGATATCTCTGGATGTTATATTCTACGGCCATGGTCAATGGCCATTTGGGAGATTATGCAA

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 3
gtattatgagccgtttagtggtttatgcttgccttttttacctgatctgtgttcggtcaaagttgctcgttcgtcctgatctgatcttgtttcactgtgtgacaattttgagtacggtgtgtgttttggttgactttgggtttggattaatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                          ||||   |||||| |  ||  ||||   | |     | || ||| | ||| |   |||   | | |||    |  ||    | |  | |  |||||| ||||  |         |||||   || ||||  ||||||||||| ||||||||||| || || || || ||||||||||| ||| | |||||| | |||||||  ||||||
------------------------------------------tgattcatgttcgatataa--tgcttccttgct---agct-atcatattttagaatgtacaagtattgttgcccttgaccatctaagctttctttgg-tttgttt---------agGTTTGCGTCAATGGTGAAATGATTGAGTACTATGATATATCAGGCTGTTACATTCTGAGGCCATGGACTATGGCAGTCTGGGAGACGATGCAA

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|213588977|gb|DB971514.1|DB971514
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattatgag ... aatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
EST: gi|213610669|gb|DB961144.1|DB961144
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattatgag ... aatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
EST: gi|209724628|gb|BW677721.1|BW677721
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattatgag ... aatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
EST: gi|192304983|gb|FG996115.1|FG996115
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattatgag ... aatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
EST: gi|192330459|gb|FK022646.1|FK022646
EST:     TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAG                         GTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT
genomic: TAGGTCTCACGCATCGGAAGGCGGAGAACTTCGGAGAGTGGTATTCCGAGgtattatgag ... aatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttgagtacggtgtgtgttttggttgactttgggtttggattaatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA
                                         gattaat  putative branch site (score: 3)
                                          attaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatgagccgtttagtggtttatgcttgccttttttacctgatctgtgttcggtcaaagttgctcgttcgtcctgatctgatcttgtttcactgtgtgacaattttgagtacggtgtgtgttttggttgactttgggtttggattaatctggcagGTTGTTGTTAATGCCGAAATGATTGAATACTATGATATTTCCGGTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA