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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctgttttttataactatggttacaagtagttttttgttttgtcatttgtgaaatcactgacaagtttgttgcatgcatcaaatattaattttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT

Basic information

species Glycine max
transcript GLYMA01G27200.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g63250.1 (Oryza sativa), 3'ss of exon 1
gcctgttttttataactatggttacaagtagttttttgttttgtcatttgtgaaatcactgacaagtttgttgcatgcatcaaa--tattaattt---tctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
   |     |  | |||   | || |  || | ||     |  |     ||||   | ||| ||||||  |  ||  || | |   | || || |   ||| |||||| | || ||||| || ||||||||||| || ||||||||||| |||||||| |||| ||  | | |   ||   |||||||||||||||||| ||| |
--ttacgcatagttactcaagcta-atatattgttacaactcatttccagtgactacgctg-caagttcat-acactcaactatgcttttcatcttactctatagGTTCTGCAGAAGGCACTTGAAGTTTGGGATCTGCAAGTTATCCCCCTTGACTCCCCAGATGTGGGGTCATGCCTATTTGACCCTGAGCTGGAAACTGCTT

upper sequence: GLYMA01G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G148115_T01 (Zea mays), 3'ss of exon 1
--gcctgttttttat-aactatggttacaagtagttttttgttttgtcatttgtgaaatcactgacaagtttgttgcatgcatcaaatattaattttctg-tagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
   | | |  |  || |||| |   | |||  |   | | ||       | | | | | ||   | | ||   ||   | |  | |||| |  ||||||  |||||||| || ||||| ||||| ||||||||||| || |||||||| ||||| || |||| ||| | | |  ||||  |||||||||||| |||   ||| |
gttcatatgctccattaactgtaact-caaccacaatatggtacca--gtctattaca-catatagatgtacttttatttctcctaatagtttttttctaatagGTTTTGCAGAAGGCGCTGGAGGTTTGGGACCTCCAGGTTATCCCCCTTGATTCCCCAGCTGCAGGGTCGTCCCAATTTGACCCTGAGCAGGAGGTTGCTT

upper sequence: GLYMA01G27200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g01730.t01 (Vitis vinifera), 3'ss of exon 1
gcctgttttttataactatgg-ttacaagtagttttttgttttgtcatttg-----tgaaatcactgacaagtttgttgcatgcatcaaatattaattttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
   || |    | ||  |     |    |   ||||   |  || |  |||     ||  ||      | |  ||| || |||  |||||  |    | |||| ||||| | ||||| ||| |||| || ||||| || ||||| ||||| ||||| | |||||||||||||||||||||||| |||||||||||||||||||| |
---tgctgggcaaaatgaaaaactgtgggcttttttccatggtgactattgcatggtgccatattcagccaacttgatg-atgtgtcaaaattc--ctgtctgcagGTTCTGCAAAAAGCTTTGGAGGTGTGGGATCTGCAAGTGATCCCCCTTGATTGTCCAGTTGCTGAGCCTGCCCAGATCGACCCTGAGCTGGAAAATGCAT

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|213614190|gb|DB956802.1|DB956802
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|120529185|gb|EH257319.1|EH257319
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|298199006|gb|HO042369.1|HO042369
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|209696635|gb|BW666931.1|BW666931
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|19453460|gb|BM954870.1|BM954870
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|209725620|gb|BW663109.1|BW663109
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|298176210|gb|HO015615.1|HO015615
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|209720336|gb|BW672155.1|BW672155
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|23725380|gb|BU760643.1|BU760643
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|10235326|gb|BE804214.1|BE804214
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
EST: gi|209728057|gb|BW655288.1|BW655288
EST:     CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAG                         GTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC
genomic: CGGATTTCGAGTCGCACAATGTCTCGCTCGACGGGGATTTCAGCATCCAGgttcgattag ... ttttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgaaatcactgacaagtttgttgcatgcatcaaatattaattttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT
                                       tattaat  putative branch site (score: 2)
                                             ttttctgt  CT-rich tract
                                 atcaaatattaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctgttttttataactatggttacaagtagttttttgttttgtcatttgtgaaatcactgacaagtttgttgcatgcatcaaatattaattttctgtagGTTTTACAAAAGGCTCTGGAAGTTTGGGACCTACAAGTTATCCCTCTTGACTCTCCAGTTGCTGAGCCTGCCCAGATTGACCCTGAGCTGGAAAATGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
-cctgttt
- - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgca