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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatgcaatcaccattgtgctttctaataaagattgcttaaacttagtagttttggtttgctttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

Basic information

species Glycine max
transcript GLYMA19G41810.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g18970.1 (Oryza sativa), 3'ss of exon 3
--------------------gtatgatgcaatcaccattgtgctttc--taataa-agattgcttaaacttagtagttttggtttg----ctttatgtt--tatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
                     |  ||   ||   | |   | | |||  |  |   | |    ||    |||   |||||| | ||    |||  ||||  | ||||| || |||||  | ||||||||||||||||||||||| || ||||| || || || || ||||| || || || ||||||||||| |||||||| ||||
gtaagctgctagtaaatattcttggaaagaacttcaaggatacattcaatgctgtcaaagcatttctcattatgggttttgatgtgaaatcttgctgttgttttagGTGGGACCTCTCAGATGCTGGCCAGGTGGATTGTGCCTTTCAAGATCGATTGGGGATACTGACGTTGGGGAGTTCATTGTGCCAATTCCACATGTCAAGC

upper sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g49040.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------gtatgatgcaatcaccattgtgctttctaataaagattgcttaaactta------gtagttttggtttgctttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
                                                                     |    ||| ||    |   |  |||| | |      || |     ||        | ||| | ||||| |   |  || |||||||| ||||| || ||||||||||||||  ||||||| || |||||||| || ||||  || || || || || |||||||| || |||||||| ||||
gtaccaattcgccccgcagtttggtagatgatggccagattgaaaaaaagagaggcttcgcttttgcgatgcattgctatgtgaagctttgtttccagtcggccatgttctgttttgtgatgcattgttgttgtttgatgctttgttctagGTTGGTCCTCTCCGGTGCTGGCCAGGTGGCCTGTGCCTTTCAAGATCTATCGGGGACATGGATGTCGGGGAGTTCATTGTGCCGATTCCACATGTGAAGC

upper sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G006429_T01 (Zea mays), 3'ss of exon 3
---------------------------------------gtatgatgcaat--caccattgtgctttctaataaagattgcttaaacttagtagttttggtttgctttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
                                        || ||| ||||   | |  | ||||||  ||  |    ||| |    ||  |   ||   ||  |  |   ||| ||||| || ||||| || ||||||||||||||||||||||| || || || || || || || || || || || || ||||| || || |||||||| ||||
gtagtgctcactgctcagtcattttgatgaagaaggattctaggatacaatatgagctctatgctttggaaacatttctgcatgggattttttaattaatttctccct---tttttagGTGGGTCCTCTCCGATGCTGGCCAGGTGGATTGTGCCTTTCAAGGTCAATTGGGGATACTGATGTCGGCGAGTTCATTGTACCGATTCCACATGTCAAGC

upper sequence: GLYMA19G41810.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0060g01580.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtatgatgcaatcaccattgtgctttctaataaagattgcttaaacttagtagtt--ttggtttgctttat---gtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
                     ||  |  |||     |  |   |||  | | |  ||| | |   |||     ||  | |||    | |||   |||| |||||||| || || ||||||||||| |||||||| || || || || || || ||||||||||| ||||||||||| ||||| |||||||||||||||||||
gtataacatatttgatgcccatacaactcaaagctgaaagaaattttaattgattattcccttgtcttgaatcttcatgggtcaaatgtatatggtttgtagGTTGGCCCACTCCGCTGCTGGCCTGGTGGATTATGTCTCTCCAGGTCAATTGGTGACACAGATGTGGGAGAATTCATTGTCCCAATACCACATGTTAAGC

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|208250632|gb|GE043735.1|GE043735
EST:     CTGCCAGCGGTGGTGAAGTAGGAAGACTCAATGTATTTGGAGGCAATGAG                         GTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATA
genomic: CTGCCAGCGGTGGTGAAGTAGGAAGACTCAATGTATTTGGAGGCAATGAGgtatgatgca ... atgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATA
EST: gi|6727063|gb|AW311417.1|AW311417
EST:     GCCAGCTGTGGTGAAGTAGGAAGACTCAATGTATTTTGGAG-CAATTGAG                         GT-GGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTA
genomic: GCCAGCGGTGGTGAAGTAGGAAGACTCAATGTATTT-GGAGGCAAT-GAGgtatgatgca ... atgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctaataaagattgcttaaacttagtagttttggtttgctttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC
  ttctaat  putative branch site (score: 2)
                                          tttatgtttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatgcaatcaccattgtgctttctaataaagattgcttaaacttagtagttttggtttgctttatgtttatagGTTGGGCCTCTTCGCTGCTGGCCAGGTGGATTGTGCCTATCTAGATCTATAGGTGACACAGACGTGGGAGAATTTATTGTGCCAATACCACATGTTAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA