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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattaagttcactaaagagaaactgtgtatctttttttttttgtgtgtgtatgtaactttttgtgtgtgtgtgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTACATTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCT

Basic information

species Glycine max
transcript GLYMA19G36680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36680.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G134862_T01 (Zea mays), 3'ss of exon 2
-------------------gtgattaagttcactaaagagaaactgtgtatctttttttttttgtgtgtgtatgtaactttttgtgtgtgtg----tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTACATTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCT
                    ||||  |  |   |  || |  |  |   |||   || |         ||| |     ||  ||||| ||      ||||  |||||||||||| |||||||| || |||||||||    ||||| || |||||| |||| ||||||||||| || |||||  |||| |||  |||    || || 
gttaattgcttcatccatattgatacatctgtttccagggtgatagca-atcgggttgtcgaaagcgatgtgtcatggttcatgtgtttggagggttgtggcttagGTACCATGCTGATTGGAGGACTGAGACACATATGGTAGTGTCGATGCTTGCATTCATGCACTGGCTGGAGACAGGTGGCCTACTCATGCATGCTGAAGCC

upper sequence: GLYMA19G36680.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0040g01630.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------gtgattaagttcactaaagagaaactgtgtatctttttttttttgtgtgtgtatgtaactttttgtgtgtgtgtgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTACATTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCT
                        |  |||  ||   | |   | |  || || |  ||  ||| || |    | |   || |  |||||  |||     ||||||||| |||||||| |||| ||||||||||||| | | ||| ||| |||| || |||||||| ||||| ||||||||||  |||||   ||| |  || || 
atgctattgttattattacttttattgttatttttgttgagttgtatatg-gttttattagtttcttataaaagaactgaaatccttgtgcttgt-----atttagGTATCATGGTGAGTGGAGGAGTGAGACACAGACAGCAGTCTCATTGCTCACGTTTATGCATTGGCTAGAAACAGGAAATCTTCTTATGCATACTGAAGCC
















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|7232984|gb|AW568335.1|AW568335
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGTGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|4396621|gb|AI495618.1|AI495618
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGNGCAATACTATAG                         GTACCATGGTGATTGG
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGG
EST: gi|151394863|gb|EV264734.1|EV264734
EST:     TATAAGCAACTTGCTGAAGCTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|298177419|gb|HO023552.1|HO023552
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|209727236|gb|BW655247.1|BW655247
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|193655938|gb|FK606624.1|FK606624
EST:     CCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: CCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|298171306|gb|HO016338.1|HO016338
EST:     TACAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGCGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|151397327|gb|EV267200.1|EV267200
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCTCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|192300429|gb|FG991471.1|FG991471
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|192332843|gb|FK026844.1|FK026844
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACGCAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|8283491|gb|BE021050.1|BE021050
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|192325592|gb|FK019448.1|FK019448
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|298191793|gb|HO035875.1|HO035875
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|192332844|gb|FK026845.1|FK026845
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACGCAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|151408235|gb|EV278043.1|EV278043
EST:     TATACGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|298166913|gb|HO010352.1|HO010352
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|6915285|gb|AW396815.1|AW396815
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|298180406|gb|HO021959.1|HO021959
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
EST: gi|4313839|gb|AI460958.1|AI460958
EST:     TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAG                         GTACCATGGTGATTGAAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC
genomic: TATAAGCAACTTGCTGAAGTTGTTGGAGGATGCCCTGGGCAATACTATAGgtgattaagt ... tgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctttttttttttgtgtgtgtatgtaactttttgtgtgtgtgtgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTACATTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCT
                        atgtaac  putative branch site (score: 3)
     tttttttttttgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattaagttcactaaagagaaactgtgtatctttttttttttgtgtgtgtatgtaactttttgtgtgtgtgtgtgatttagGTACCATGGTGATTGGAAGAGTGAGACACAGTCTGTAGTTTCAATGCTTACATTTATGCACTGGCTTGAAACAGGAAGCCTTCTCGAGCACAAAGAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG