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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttaatgtattatagttctatacttgctgtgtttatcttgcctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC

Basic information

species Glycine max
transcript GLYMA07G39380.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 10
gtgcttaatgtattatagttctatacttgctgtgttta--tcttgcctgtaatgcaatttgactaagcctc--aatgttggtatatatttccattt--agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC
     |||    ||||||| ||    | ||||   | |  | ||||     |     |   |||||| | |  | || || |  | ||||   |||  ||||||| || || |||||||||||||||||||||   |||||||| ||||| ||||||||||||||     |||| |  ||    | |   || || || |
----gtaaacagttatagtcctcccttcgctgacatgactttttgctgaagagttggtcatactaagtccctaactggtgttggaaatttttgtttttagGTTGCAAAAATTGAAACAGAGAAAATGCTTATTGCCATGGTTGAGACTGAATTGGAGAAGAGAAAAGCTGAGGGGAAGTACCCCGCACATTTCAGAGGCC

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 3
----------------gtgcttaatgtattatagttctatacttgctgtgtttatcttgcctgta--atgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC
                 || ||||  |  | | | ||| | ||  | |  ||  |  |||    |  || | | |    ||  | |      | || |   | |   |||||||||| || || ||||| |||||||||||||||   ||||| ||||||||  |||||||||||||     |||| | |||    | |   || || || |
gtaaagactgggaatattgtttaactt--tcttggtctcttctaacaggattctttctgctgaaaggataccagtaacttagacatgctcactagtct---tgttgttttagGTTGCAAAAATTGAAACTGAGAAAATGCTTATTAGCATGGTGGAAACTGAACTGGAGAAGAGAAAAGCTGAGGGGAGATACTCTGCACATTTCAGAGGAC

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 10
gtgcttaatgtattatagttctatacttgctgtgtttatcttgc-ctgtaatgcaatttgactaagcc--------tcaatgttggta----tatatttccattt----agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC
     ||||  || || || || | ||    ||  | |  || | |   |||||| || |  | | |         ||| | ||  ||     || |   ||| |    ||||||| ||||| || || ||||| |||||||||||||||||||||||||| |||||||| |||||||||   ||  |||| || |||  ||| | ||| |
----gtaattgatcatggtcctgt-ctcctcgtactaaatttccaccacaatgcagttagcttcatctctcacaaatcattattaataataccatgtcctcatctcaatagGTTGCTAAGATTGAGACTGAGAAGATGCTTATTCAAATGGTTGAAACTGAATTGGAGAAAAGAAAGCAAGCTGGTGCATACAAGGGACAATTCATGGGAC

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
lower sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------gtgcttaatgtattatagttctatacttgctgtgtttatcttgcctgtaatgcaatttgactaagcctcaatgttggtatatatttccattt-agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC
                   |   | ||  |    | ||  |    |      |  | |   |  | | || ||      | |   | ||  ||  |||  |||| |  || ||||||| || ||||| |||||||||||| | ||||||||||||||||| ||| | ||||| |  |||  | |||| |||||| || | |  || | |||| 
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
gtgcttaatgtattatagttctatacttgctgtgttt--atcttgcctgtaatgcaatttgactaagcctcaa--tgttggta-tatatttccat---ttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGG-AGGATTTAGGGGGC
||| |||   ||| ||  |  ||||  || ||| |||  |  || | |||  || ||||    ||   ||     | ||| || | | |||  ||   ||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| |||    |||||||||| |||   |    | |      
gtgtttatcttat-atgctagtatatgtg-tgtatttgaactttacttgtt-tgtaattctgatagatctttggttattgataatctgtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA-

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|254342634|gb|GR858796.1|GR858796
EST:     CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|151402902|gb|EV272715.1|EV272715
EST:     GCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: GCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|26058870|gb|CA801784.1|CA801784
EST:     CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
genomic: CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG
EST: gi|193420756|gb|FK385793.1|FK385793
EST:     CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTAGACCAAGATAGAAACA
genomic: CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTT-G-CCAAGATAGAAACA
EST: gi|298181953|gb|HO026128.1|HO026128
EST:     CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAG                         GTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAAAGGTTGAAACTGAG
genomic: CAATTCAAGAACAATTAATGCTTGAAAGAGATCCGCATGGAAATGTTCAGgtgcttaatg ... ttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC
               atttgac  putative branch site (score: 4)
                                            tttccattt  putative PPT
                                      tatatatttccattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttaatgtattatagttctatacttgctgtgtttatcttgcctgtaatgcaatttgactaagcctcaatgttggtatatatttccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT