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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgtttcatgctttaatacattctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC

Basic information

species Glycine max
transcript GLYMA09G37080.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 6
gtattttgtttcatgctttaatacattctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
    | || || |   ||| |||| |  || || |  |  || |   |   | || ||| |   |   | | ||| |  || ||||||||||||||||||  || || |||||||||||||||||||||||||| || || || |||||||||||||| || || ||||| || |
---gtatgctttaacatttcatac-tattcgttgtgttctttctc--tccttccttacagtgg-aggttatgcagCCCACTTTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTGCTTTTGGCTTCAATAGAGAACATGCAGTATGCTGTGACGGTGGATGTTCTAC

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 6
----------------------gtattttgtttcatgctttaataca---ttctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
                        ||  |||||||  |   ||  ||    || ||  ||  || |||||  |         | |    | ||| | ||| |  |||||||||||||||||||||  || || |||||||||||||| ||||| || || ||||| || ||||| |||||||| || || ||||| || |
gtatgcttcatatgttcatatctcatgatgtttcaccccccaacccacccctcccccctttttaatttttgttgctcttactctaaaggaaaatttgcagCCCACTGTAGGCCCTGATGGGAAGATAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACGGTGGATGTTCTGC

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G082174_T05 (Zea mays), 3'ss of exon 4
-----------gtattt-tgtttcatgctttaatacattctccttttactactttttagtatgtgctaac-aatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
            | ||  | | || || | |   ||   ||| ||||   |  ||||  |   |||| ||  |    | ||| | ||| |  | || |||||||||||||||   || || |||||||||||||| ||||| || || ||||| || ||||| |||||||| || || ||||| || |
gtttgcttcatatgttcatatctcgtgatgtttcaccccctctttttttaaagtttttatggctgcttactgaaaggaaaatttgcagCCCACGGTGGGCCCTGATGGGAAGGTAAAGGAGCCTGAGAGCAATGTACTTTTAGCATCAATTGAGAACATGCAATATGCTGTGACAGTGGATGTTCTGC

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 6
gtattttgtttcatgctttaatacattctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
|||  || ||| |   || ||||        || |   | ||||||  |||| ||||||    | |  | | ||| ||||| |||| |||||||| ||||  |||||||||||||| ||||| ||| | ||||| ||||| |||||||| ||||||||||| || ||||| || |
gtaaatt-ttttacagttgaatat-------ttattgaaatttttaccatgtactaacaggt-tgttctatccagCCTGCTTTAGGTCCTGATGGCAAGAAAAAAGAACCTGAGAGTAATGTTCTTCTTGCTTCAATTGAGAATATGCAATATGCTGTTACAGTAGATGTTCTTC

upper sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S81_184V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------gtattttgtttcatgctttaa---------tacattctccttttactactttttagtatgtgctaacaatcatataatcttca---gACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
                          ||||  | |||||  | ||         |  ||| ||  | |   | | ||   |   || | |   |    |  | | ||   |  |   || || |||||||| |||||||  || |||||||||||||||||  | | ||| |||||||| |||||||| || || ||  |||| ||  | |
gttagtatacacacttgtcccttgaaatttcatatcatgtatgaagagtgcctatggattttcgctctttcaatcttacattcatgttcattctatggttgtttgcaacagTTTAGCGTTGGACCTGATGGAAAGAGGAGGGAGCCTGAGAGCAATGTGCTGCTTGTTTCAATTGAAAACATGCAGTACGCCGTAACGATTGACGTAATAC

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|207809609|gb|GD782313.1|GD782313
EST:     ACCGCTATTGAGGGGGCAGTACAG                         ACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTT
genomic: ACCGCTATTGAGGGGGCAGTACAGgtattttgtt ... taatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTT
EST: gi|208048447|gb|GD844886.1|GD844886
EST:     CAAATCCCATGCTTCCTGTTAATTATACCGCTATTGAGGGGGCAGTACAG                         ACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTT
genomic: CAAATCCCATGCTTCCTGTTAATTATACCGCTATTGAGGGGGCAGTACAGgtattttgtt ... taatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacattctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC
                               tgctaac  putative branch site (score: 1)
                                                tcttc  putative PPT
           ttttactacttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttgtttcatgctttaatacattctccttttactactttttagtatgtgctaacaatcatataatcttcagACTGCTGTAGGCCCTGATGGGAAGAGGAAAGAACCTGAGAGCAATGTGCTTTTGGCTTCCATTGAAAATATGCAGTATGCTGTTACTGTTGATGTCCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT