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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA

Basic information

species Glycine max
transcript GLYMA11G12610.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgt-atattacaa----acagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
                          ||  ||||| | |  ||| |  || ||         ||  | ||  | ||  |     | |   |||| ||| |  |||||||||||||| || |||||  | ||||||||||||||||| ||||||||||||||  | |||||||| ||  | || ||||| || ||||  ||   ||
-------------------------gttggtgaatgttgattgttactttgcagttctctgcagtctatggatctttgaaagtgtctgtgttacatttgttgcagGTTATCATCGTGACCAGCTCGTTGATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCTAATGCAATAAGAGTTCTTTGCCGCATCATTGACTCAA

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
           |  |||| | |  | |||    || |||| ||   |  | ||   |  ||   ||     || ||  || |  | |  |   |    |||| ||||| || ||||||||| | ||||||||||||||||| || |||||||||||| | || ||||||||| | || ||||||||||| |  ||   ||
---------gttggtgacta-ttggtttctactatgtggtttggcaa--ataatgtggaatgtggaaatgactttcatttgtgatctgttgggt--gtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACTGATATGTACCGTGCAAATGCTATTAGAGTTCTTTGTCGTATTATTGACTCAA

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
           |  ||| || |  | | |    || ||||  |   | || |    ||   |  |  ||   |  |  || |  | || |   |    |||| ||||| || ||||||||| | ||||||||||||||||| || || ||||||||| | || || |||||| | || ||||||||||| |  ||   ||
---------gttggtgaaca-ttggttgctactatgtggttcggcaaata-atgtggaatgtggggatgactt-ccatttgtgatctattgggt--gtagGTCATCATAGTAACAAGCTCTTTGATGAAGGACATGAATAGCAAAACCGATATGTACCGTGCAAACGCTATTAGAGTTCTTTGTCGTATTATCGACTCAA

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G012501_T01 (Zea mays), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
|||| | |   | |||     ||||||    |||||   | | | |  | |   |  |   ||| | |     ||   ||   |||||   || ||| |||| ||||| || ||||||||  | ||||||||||||||||| ||||| ||||||||| | || ||||||||| | || |||||| | || |  ||||| |
gttaaataaa-tgatgttt--tcagat----gaatacaatgtttttgatgccttctaa---tctaattaaaagatgg-ttgagctttatgattgtaatagGTCATCATAGTCACAAGCTCATTGATGAAGGACATGAATAGCAAGACAGATATGTACCGTGCCAATGCTATTAGAGTTCTTTGTAGAATAATTGATGGTA

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 3
-gttacaaattctcatgaccagtcagattcatgaatatggtc-tgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
   |  ||||| |  |   || |   | | | ||| || |||     ||||  |   | |  ||||||      ||  |  ||   |||  ||     | ||||||||||||| ||||||||||| |||||||| ||||||||||| | |||||||||  | || |||||||| |||||||| || || || | ||| ||||
gtctgtaaattttact---caatttcaat-acgaacatcgtcgcacttattgtaggtatattttctga------taagttgttggtttt--ttcgcccatagGTTATCATCGTAACAAGCTCTCTGATGAAGGATATGAATAGTAAAATTGATATGTATCGAGCAAATGCTATCCGTGTCCTCTGCCGGATAATAGACGGAA

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
|||| |     |  ||     |  | ||  |   ||    || ||| ||   || || |   ||||||| | |||   || ||         |  || ||||||| || || || ||||| || ||||||||||||||||| ||||||||||||||  | || ||||||||||| || || ||||| || || |||||||
gttaaattgattgttgttttatttg-tttgtttgtaccaactttat-ttgtgaaaagtg---ctgactggtttataatttata---------tacaaaagGTTATTATTGTGACTAGCTCACTTATGAAGGACATGAATAGCAAGACTGATATGTATCGAGCAAATGCTATTCGGGTTCTCTGTCGAATAACGGATGGAA

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ15122 (Selaginella moellendorffii), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
                                          |||   |      |  |  | ||       |   | |   || |  ||||  | |||||||||||| || |||||||| || |||||||||||||    |||||| ||| | ||| | || ||||| ||  | || |||||| | || ||||||||  
------------------------------------------gtaagctcgtggaaacgcctttggaaaggtt--ttttaagacatagctttgctgacagGTTATCATAGTCACAAGCTCGCTGATGAAGGACATGAGCTCTAAGACGGATCTCTACCGAGCAAATGCAATAAGGGTGCTTTGTAGGATTACAGATGGTG

upper sequence: GLYMA11G12610.2 (Glycine max), 3'ss of exon 4
lower sequence: EFJ08461 (Selaginella moellendorffii), 3'ss of exon 4
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
                                          |||   |      |  |  | ||       |   | |   || |  ||||  | |||||||||||| || |||||||| || |||||||||||||    |||||| ||| | ||| | || ||||| ||  | || |||||| | || || |||||  
------------------------------------------gtaagctcgtggaaacgcctttggaaaggtt--ttttaagacatagctttgctgacagGTTATCATAGTCACAAGCTCGCTGATGAAGGACATGAGCTCTAAGACGGATCTCTACCGAGCAAATGCAATAAGGGTGCTTTGTAGGATTACCGATGGTG

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|120529501|gb|EH257635.1|EH257635
EST:     GGAGAATGGTCTACCTGATCATAAAGGAACTCTCCCCTTCTGCAGATGAG                         GTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGAT
genomic: GGAGAATGGTCTACCTGATCATAAAGGAACTCTCCCCTTCTGCAGATGAGgttacaaatt ... tttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGAT
EST: gi|193355637|gb|FK323414.1|FK323414
EST:     GGAGAATGGTCTACCTGATCATAAAGGAACTCTCCCCTTCTGCAGATGAG                         GTTATCATCGTTACA-GCTCTCTCATGAAGGACATGAATAGTAAGACTGAT
genomic: GGAGAATGGTCTACCTGATCATAAAGGAACTCTCCCCTTCTGCAGATGAGgttacaaatt ... tttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA
               ttctgac  putative branch site (score: 2)
                     ctgttctatctctttt  CT-rich tract
                               tcttttactttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacaaattctcatgaccagtcagattcatgaatatggtctgtatattacaaacagagattctgactgttctatctcttttactttacttttttaacagGTTATCATCGTTACAAGCTCTCTCATGAAGGACATGAATAGTAAGACTGATATGTACAGGGCTAATGCTATTCGTGTCCTTTGTCGTATCACAGATGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA