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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctccagtaaatgatcctatatggttatgcactgtttttccttttgctaatgcaatctgttcaccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATTTCTCATCGGGAAGCAGATAAGCGAGGAAAGATATATGACCGTGAAAATT

Basic information

species Glycine max
transcript GLYMA11G05760.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os06g16390.1 (Oryza sativa), 3'ss of exon 14
---gtattctccagtaaatgatcctatatggttatgcactgtttttccttttgctaatgcaatctgttcaccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATTTCTCATCGGGAAGCAGATAAGCGAGGAAAGATATATGACCGTGAAAATT
     |||   |  |  |   |  |      | ||     ||     | | |    |  |  | |  | |  || |||||||||||||| ||||| || || ||||| ||||| ||||| ||| | || || |||   ||||| || ||||| |||||||||||||||||||| ||||
gtaagatttctctattgacccttttcctccctcataggacgtaccctcatctaactagtccttttcctaaatcttcagAATAGTGTTGGGAAGCACGAGTATCTTGGCGAGTACACTGGGGAGCTTATCTCCCATAAAGAAGCTGACAAGCGTGGAAAGATATATGACCGTGAGAATT

upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G157820_T02 (Zea mays), 3'ss of exon 14
gtattctccagtaaatgatcctatatggttatgcactgtttttccttttgctaat--gcaatctgttcaccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATTTCTCATCGGGAAGCAGATAAGCGAGGAAAGATATATGACCGTGAAAATT
|||        ||  || || | | || |  | |  |   ||    ||  || ||  |   | | || | ||| |||||||||||| | || |||||||||||||| ||||| ||||| ||  | || || ||    |||||||||||||| |||||||||||||| ||||| || |
gtaaaactatatatctgttcttttgtgttcgtactttcccttgatgttgtcttatttgtcttttcttaaaccttcagAATAGTGTTAGCAAACATGAATACCTTGGTGAGTACACTGGGGAACTAATCTCACACAAAGAAGCAGATAAGCGTGGAAAGATATATGATCGTGAGAACT

upper sequence: GLYMA11G05760.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv07s0031g00320.t01 (Vitis vinifera), 3'ss of exon 12
-----gtattctccagtaaatgatcctatatggttatgcactgtttttccttttgct-aatgcaatctgttcaccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATTTCTCATCGGGAAGCAGATAAGCGAGGAAAGATATATGACCGTGAAAATT
      || | | ||  | ||| | || | | |    ||   || | ||    |||| |||      | ||||  || ||||||||||| || || |||||||| ||||| ||||| ||||||||  ||||||| ||  |||||||||||||||| |||||||| ||||||||||||||||
gtaacataatgttcaa-atatggtgctgtttcgg---gcttggtatctctagctgctgaataatgctttttcattcttcagAATAGTGTGGGCAAACATGAATATCTTGGTGAGTACACTGGAGAACTGATTTCACACAGGGAAGCAGATAAGCGTGGAAAGATTTATGACCGTGAAAATT

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|208232711|gb|GE029944.1|GE029944
EST:     CGGCTGGGGAGCCTTCTTAAAG                         AATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
genomic: CGGCTGGGGAGCCTTCTTAAAGgtattctcca ... caccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
EST: gi|23063121|gb|BU578542.1|BU578542
EST:     GTTCTTCTTGGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAG                         AATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
genomic: GTTCTTCTTGGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAGgtattctcca ... caccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
EST: gi|22932691|gb|BU549830.1|BU549830
EST:     TGTATCCGGCTGGGGAGCCTTCTTAAAG                         AATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
genomic: TGTATCCGGCTGGGGAGCCTTCTTAAAGgtattctcca ... caccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
EST: gi|208261748|gb|GE059515.1|GE059515
EST:     GGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAG                         AATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
genomic: GGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAGgtattctcca ... caccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
EST: gi|254325926|gb|GR838807.1|GR838807
EST:     CTTGGAAGGTCTGATGTATCCGGCTGGGGAGCC-TCTTAAAG                         AATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
genomic: CTTGGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAGgtattctcca ... caccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
EST: gi|254327703|gb|GR834668.1|GR834668
EST:     GTTCTTCTTGGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAG                         AATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT
genomic: GTTCTTCTTGGAAGGTCTGATGTATCCGGCTGGGGAGCCTTCTTAAAGgtattctcca ... caccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatatggttatgcactgtttttccttttgctaatgcaatctgttcaccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATTTCTCATCGGGAAGCAGATAAGCGAGGAAAGATATATGACCGTGAAAATT
                            tgctaat  putative branch site (score: 2)
                                       tctgttcaccctcc  putative PPT
                tgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctccagtaaatgatcctatatggttatgcactgtttttccttttgctaatgcaatctgttcaccctccagAATAGTGTTGGTAAGCATGAATACCTTGGAGAGTATACTGGAGAGTTGATTTCTCATCGGGAAGCAGATAAGCGAGGAAAGATATATGACCGTGAAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT