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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgagggaacaattaattgcattactttctcatttcagaaaatctttgtactgtgacactatgtatattaacagcaaatataattttccttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT

Basic information

species Glycine max
transcript GLYMA20G32260.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0019g04660.t01 (Vitis vinifera), 3'ss of exon 11
actgagggaacaattaattgcattactttctcatttcagaaaatctttgtactgtgacacta-tgtatattaaca----gcaaatataattttccttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
       | || |||  || ||| ||  ||  |||    ||    ||  |  | ||   ||  | |||   |  |       | |||  ||||   |  || ||||| |||||||| ||||||||||||| || |||||||||||||| 
----tccgtaccatttctt-cataaccctcggattatttaagcctttgatcttttgctgctcctttattccactatgtcatcattatccttttatctggttgcagGTTTGGTGATGGCATTGATTGGATCTTTGCTCACAATGCTTGTA
















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|58019707|gb|CX706449.1|CX706449
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|209702870|gb|BW655992.1|BW655992
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|16104867|gb|BI892607.1|BI892607
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|209702922|gb|BW656019.1|BW656019
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|9819649|gb|BE555162.1|BE555162
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|58017037|gb|CX703779.1|CX703779
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|209710224|gb|BW653602.1|BW653602
EST:     AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: AGGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCTTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
EST: gi|15202138|gb|BI425242.1|BI425242
EST:     GGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCCNNNNNNNG                         GTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
genomic: GGGTTGGTACTTTCTACCCTGGTTATTGGTCTCTCAGTTCCC-TTTTTTGgtaagtcttt ... ttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtactgtgacactatgtatattaacagcaaatataattttccttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT
                     tattaac  putative branch site (score: 1)
                                       ttttccttttttac  putative PPT
               tatgtatattaacagc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgagggaacaattaattgcattactttctcatttcagaaaatctttgtactgtgacactatgtatattaacagcaaatataattttccttttttacagGTCTGGTGATGTCATTGATTGGATCATTACTCACAATGCTTGTT

- -gagggaa
- - - - - - - - - -gcattac
- - - - - - - - - - - - - - - - - - - gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgacact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatataa