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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagtttgaatcgaagtggtgcaagttggttcagagtctatgtttttcgaggttgtctgatgcgttaccccaattgatattcttttgctgttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCC

Basic information

species Glycine max
transcript GLYMA17G12250.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12250.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g40370.1 (Oryza sativa), 3'ss of exon 10
tcaagtttgaatcgaagtggtgcaagttggttcagagtctatgtttttcgaggttgtctgatgcgttaccccaattgatattcttttg----ctgttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCC
    |  | ||  | |||  |      |   | |   | | || |        |  ||  |||   | | |   |||  ||  |  ||     | |  |   |||| | ||| || || |||||||||||||||||  | |||||||||||   |||| |  || ||||||||| |||||| ||| | ||||||||||||||||
---tgcattaactgcagtcctcatgaataacttatgttgtctgatgca-actttcatcacatggagtgctcatgttgcaataatgatgggttttatatttgtagGAGTTTGTCAAACGTCAAACTCGTTTTGTCTCAAGGAAACCAGCAAAGACTATAGTAGCTACAATTGAAGTTGTTGCTGAGACTATGGGTCTTAAGGTCC

upper sequence: GLYMA17G12250.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G137569_T02 (Zea mays), 3'ss of exon 9
tcaagtttgaatcgaagtggtgcaagttggttcagagtctatgtttttcg---aggttgtctgatgcgttaccccaattgatattcttt-tgctgttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCC
   | ||||      |    |   |||   |   ||    | | || ||    ||  | ||| |||| |     ||    || || |||    | ||     |||| ||||| ||||| ||||| |||||||||||  | |||||||| ||   |||| |  || ||||||||| |||||| ||||||||| |||| |||||||
---aatttgctctacacatatctcagtccttatggataacaggcttatcatttagtctatctaatgcctc-ttgcatcacatgttttttactttttttctgtagGAGTATGTCAAGCGCCAAACGCGTTTTGTCTCAAGAAAACCAGCTAAGACTATAGTAGCTACAATTGAAGTTGTTGCCGAGTCAATGAGTCTCAAGGTCC

upper sequence: GLYMA17G12250.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g05420.t01 (Vitis vinifera), 3'ss of exon 11
tcaagtttgaatcgaagtggtgcaagttggttcagagtctatgtttttcgaggttgtctgatgc---gttaccccaattgatattcttttgctgttc--taacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCC
  | | |  | |     || ||   | |  |   |||||  |     | ||  || |    ||    | || |     |  || |  ||||   |    |  |||||||||||||| ||||||||||||||||| |||||  ||||||||||||||||||||||| | ||||||||||| ||||| || |||  | | |||||||
-taggct--agttagtatgttgtttgataat--ggagtccttaaccattgacattcttctttgtctagctatcatgcattctaattatttgggatctggtggcagGATTATGTAAAACGGCAAACTCGTTTTGTTTCCCGCGAACCAGCAAAAGTTATAATTTCTACTATTGAAGCTGTGGCAGAATCTATGAATTTCAAGGTCC

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|7693020|gb|AW761119.1|AW761119
EST:     TTGCTNTATCACAANGGTTGAATCTTTCACCACTATTTGATAGGCATCAG                         GATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCCGTAA-CCAGCAAAAGT
genomic: TTGCTTTATCACAAGGGTTGAATCTTTCACCACTATTTGATAGGCATCAGgtattgtttt ... gttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCC-GTAAACCAGCAAAAGT
EST: gi|58019760|gb|CX706502.1|CX706502
EST:     ATCACAAGGGTTGAATCTTTCACCACTATTTGATAGGCATCAG                         GATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTT
genomic: ATCACAAGGGTTGAATCTTTCACCACTATTTGATAGGCATCAGgtattgtttt ... gttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTT
EST: gi|57574558|gb|CX547533.1|CX547533
EST:     TGCTTTATCACAAGGG-TGAATCTTTTCACCACTATTTGATAGGCATCAG                         GATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTT
genomic: TGCTTTATCACAAGGGTTGAATC-TTTCACCACTATTTGATAGGCATCAGgtattgtttt ... gttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgaggttgtctgatgcgttaccccaattgatattcttttgctgttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCC
                           aattgat  putative branch site (score: 4)
                                   ttcttttgctgttct  CT-rich tract
                           aattgatattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaagtttgaatcgaagtggtgcaagttggttcagagtctatgtttttcgaggttgtctgatgcgttaccccaattgatattcttttgctgttctaacagGATTATGTAAAGCGGCAAACTCGTTTTGTCTCCCGTAAACCAGCAAAAGTTATAATTTCTTCAATTGAAGCTGTTGCAGAGTCAATGGGTCTTAAGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT