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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttcttgtggctctagtttcaagtttgattcttctttatacagccttgaagaatagtttttgccctcccccctccccctcctatacagcctatgttaatagttttgtcatatctagtcactcttggtttaacgttgtcaaactttggaccatggatctacctgtacatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTGCTGAGGCTCTAGAATATGGACTTGTGGGTGTTAATGAAGGAGTAATTTC

Basic information

species Glycine max
transcript GLYMA15G41690.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv19s0085g00870.t01 (Vitis vinifera), 3'ss of exon 16
gtagttcttgtggctctagtttcaagtttgattcttctttatacagccttgaagaatagtttttgccctcccccctccccctcctatacagcctatgttaatagttttgtcatatcta-gtcactcttggtttaacgttgtcaaactttggaccatggatctacctgtacatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTGCTGAGGCTCTAGAATATGGACTTGTGGGTGTTAATGAAGGAGTAATTTC
                                                                      |    ||   |||| | |   | |  || ||| | ||| | | |   |  ||  ||| |  |||   |  |     |||    ||||     ||   ||    || |||||| | | | || || || ||||| |   | |||||||| ||||||||  |||| | ||| |||||||||||||| ||||| | ||||||| ||||| |
-----------------------------------------------------------------atggtcttaatcattctcccaaatgtcatg-gtaaatggatttatgaaaaggatatccatctagacttataatcatgtgttttt----catg-----acacatat---tgcagGTTTAGCTGCCTATATTTTCACAAAAAACCTACAACGATCTTGGCGTGTCTCTGAAGTTCTTGAATATGGACTTGTTGGTGTCAGTGAAGGATTAATTCC
















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|48574885|gb|CO036126.1|CO036126
EST:     ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG                         GTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
genomic: ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAGgtagttcttg ... acatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
EST: gi|151400125|gb|EV269939.1|EV269939
EST:     ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG                         GTT-GGGTTCATACATATTTACAAA
genomic: ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAGgtagttcttg ... acatatgaagGTTTGGGTTCATACATATTTACAAA
EST: gi|7146475|gb|AW508397.1|AW508397
EST:     ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG                         GTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
genomic: ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAGgtagttcttg ... acatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
EST: gi|151404401|gb|EV274211.1|EV274211
EST:     ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG                         GTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
genomic: ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAGgtagttcttg ... acatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
EST: gi|208239673|gb|GE039165.1|GE039165
EST:     GAATTGCTAACGACACTAATGCAG                         GTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
genomic: GAATTGCTAACGACACTAATGCAGgtagttcttg ... acatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
EST: gi|298198520|gb|HO040059.1|HO040059
EST:     ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAG                         GTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG
genomic: ATTCAAAACTGAAGAGGATGCTATCAGAATTGCTAACGACACTAATGCAGgtagttcttg ... acatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttggtttaacgttgtcaaactttggaccatggatctacctgtacatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTGCTGAGGCTCTAGAATATGGACTTGTGGGTGTTAATGAAGGAGTAATTTC
      gtttaac  putative branch site (score: 3)
                   aaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttcttgtggctctagtttcaagtttgattcttctttatacagccttgaagaatagtttttgccctcccccctccccctcctatacagcctatgttaatagttttgtcatatctagtcactcttggtttaacgttgtcaaactttggaccatggatctacctgtacatatgaagGTTTGGGTTCATACATATTTACAAACAGTATCCAACGATCATGGCGTGTTGCTGAGGCTCTAGAATATGGACTTGTGGGTGTTAATGAAGGAGTAATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG