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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgaatctttgtctactgaatctaatttagtatcttataacatatggctgattagtttctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os10g08550.5 (Oryza sativa), 3'ss of exon 10
--------------gttgaatctttgtcta---ctgaatctaatttagtatctt--ataacatatggct---gattagttt------ctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG
               || | |  |||| ||    |     ||| ||| | | ||  ||    |  ||||   || |  |||      ||  | |   ||||||| ||||| ||||||||||||||||| ||||| ||| || ||||||| |||||||||||| | || || ||||| |||
gtttgtgtactttgattaatttattgtttatctttctgcataagttaatgtttttgattgactgaggcttgagactttttttgcaacctgatatggtagGTTGTCATTGGAATGGATGTTGCTGCTTCGGAATTCTACAATGACAAGGACAAAACCTATGACCTTAACTTCAAGGAGGAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 7
-----------------------------gttgaatctttgtctactgaatctaatttagtatcttataac--atatggctgattagtt--tctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG
                              ||  ||  || |   || |  | | || | | ||| | |     |||||    ||| ||   ||  | |  |||||||| |||||||||||||||||||||||||| || |||  | |   |||  ||||||||||  | || || |||||||||
gtttgttgagcatacaactggctaaattaatttgatggttatgggctaaggc-acttcaatttctgacatttggtatggaatgttatttgtactgatatgccagGTTGTCATTGGGATGGATGTTGCTGCTTCAGAGTTCTACACTGA---GGACCAAACCTATGATCTTAACTTCAAGGAAGAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G048371_T01 (Zea mays), 3'ss of exon 11
----gttgaatctttgtct-actgaat-ctaatttagtatct----tataacatatggctgattagtttctattcttac---agGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG
         || ||||| |   | | |  | |  |   |  |    | |  ||||||  |   |  | |||||    |    ||||||| || || ||||||||||||||||| || ||||||  | |||||||  ||||||||||| | || |||||||| |||
gttcaccagatatttgttttgttcagtattcacctgagacttgaagtttgtcatatgtttttcttatctctatctgaatgctagGTTGTCATCGGAATGGATGTTGCTGCTTCGGAGTTTTACAGTGACAAGGACCAAACCTATGACCTCAACTTTAAGGAGGAG

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------gttgaatctttgtctactgaatctaatt-------tagtatcttataacatatg---gctgattagtttctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG
                            ||  || | |    ||| | |||| ||       || ||| ||      ||      ||||||| |  || ||||| ||||||||||||||||||||||||||||||||||| || || |||||||||||||| ||||||||||||||||| |||||||||
gtaacttctctcatctttgaaatctaacttatatttcttagcacttattctatttgcatggttattatttttggttttacattcactgattattgacttttcttgcagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAGTTCTATGATAACAAGGATAAGACCTATGACTTGAATTTCAAGGAAGAG

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|254320422|gb|GR826871.1|GR826871
EST:     -TCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         -TTGTAATTGG-ATGGATGTTGCTGCTTCAGAATTT-ACGATA-CA-GGAT
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
EST: gi|254317870|gb|GR832038.1|GR832038
EST:     GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
EST: gi|16996761|gb|BM086133.1|BM086133
EST:     GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
EST: gi|24135559|gb|BU926069.1|BU926069
EST:     GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
EST: gi|58021375|gb|CX708116.1|CX708116
EST:     GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
EST: gi|254343118|gb|GR859280.1|GR859280
EST:     GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         -TTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACG
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACG
EST: gi|15812359|gb|BI784634.1|BI784634
EST:     GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAG                         GTTGTNAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGA
genomic: GTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGT-AATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGA
EST: gi|254329396|gb|GR838949.1|GR838949
EST:     TGCTAAAGCTGGTTACACTGGAAAG                         GTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT
genomic: TGCTAAAGCTGGTTACACTGGAAAGgttgaatctt ... attcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaatctaatttagtatcttataacatatggctgattagtttctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG
                                        tttctattctt  CT-rich tract
       taatttagtatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaatctttgtctactgaatctaatttagtatcttataacatatggctgattagtttctattcttacagGTTGTAATTGGGATGGATGTTGCTGCTTCAGAATTTTACGATAACAAGGATAAAACCTATGACTTGAATTTTAAGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA