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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgctcagctgataatagtcataatagaccttgcaggtctttattattgatcgtttacttgtggcttattgttaattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA

Basic information

species Glycine max
transcript GLYMA20G24430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g43576.1 (Oryza sativa), 3'ss of exon 5
gtttgctcagctgataatagtcataatagaccttgcaggtctttattattgatcgtttacttgtggcttattgt-taattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA
||||| ||       ||   |   |     | ||  |  || |  |      || |||  |  ||  || |||| | || | |      ||  |  | ||||||||       |||||    |||| ||| ||||| |||||||||||||||||||||||||| || |||||||||||| | ||||||| ||| || ||||
gtttgatctttgagcaactttgccagcg--ctttttatatcctcctggact-tcctttgttcttg--ttgttgtatcatccaatgctccttgcttatacagCCAACAGAAAGACACTTGCGGGTCAGAGAATATGTGACTCCTGAGAAGTTTGATTTCTGGAAGGAGTATGGGGAATCTCTGGGTTTTCTTTATGTTGCTA

upper sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------gtttgctcagctgataatagtcataata--gaccttgcaggtctttattattgatcgtttacttgtggcttattgttaattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA
                           |     |   |||| || || |    |  | | | |     |   || |  |   |  |  |  |||       |||    |  ||      || |||||||||| |||||  | ||||| ||||||||||| || ||||||||||||||||||||||||  ||| || ||||| || || |||||||| || || |
gtaaactaatcacttcaacattccccacatcattcgcaatattcctatttccaagatagaaagatcccaaatttcaaagaacatctacgatttaaaaccgtttctcttg--ttccacaatgaagCCAACTCCATTGCATCTGACTGTGAAAGAGTATGTCACACCTGAGAAGTTTGATTTCTGGAAAACATACGGAGAATCAATAGGATTTCGTTATGTTGCAA

upper sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 3'ss of exon 5
gtttgctcagctgataatagtcataatagaccttgcaggtc--tttattattgatcgtttacttgtggcttattgttaattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA
 |  |        | || ||       ||||   |||  ||   | | |   | ||   |  ||         | |||||   |    || | ||| ||||||||||||| || ||| | |||||||||||||||||||| ||||||||||||| ||||||||| ||||||||||| || ||||| || ||||| || ||||
ataagaggcatccacaaaagcagcctcagacaacgcacatcaactaacttcagttcaagtttttaaacagatctattaat--aagtacttatgttgctgcagCCAACTCCATTACACCTTACTGTCAAAGAGTATGTTACCCCTGAGAAGTTTGCTTTCTGGAAGGAATATGGGGAGTCAATTGGATTCCGTTATGTTGCTA

upper sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ08741 (Selaginella moellendorffii), 3'ss of exon 5
gtttgctcagctgataatagtcataatagaccttgcaggtctttattattgatcgtttacttgtggcttattgttaattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATC---TATTGGTTTTCGTTACGTAGCTA
                  ||| |||  |     || | ||    | ||| | | |||||| | | |||||         |||| ||| ||   |   |||||||||||  ||||| | || || ||||||||  | ||||| |||||||| || |||||||||||||| ||||| ||     | || ||||| ||||| |   
---------------gtaagtgatagcaa----tg-aagtgacgagtat-gcttgtttacct-tagctta---------cgaacgatcttcccg--acagCCAACTCCTGTGCACCTCACGGTGAAAGAGTACATAACTCCGGAGAAGTTCGACTTCTGGAAAGAATACGGGGAGTCAGTCGTCGGGTTTCGATACGTCG---

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|193517386|gb|FK476553.1|FK476553
EST:     CCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: CCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|21675910|gb|BQ628261.1|BQ628261
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|208182079|gb|GD979434.1|GD979434
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAA
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAA
EST: gi|208315134|gb|GE112650.1|GE112650
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|117557937|gb|EG702322.1|EG702322
EST:     GGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: GGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|208144636|gb|GD943045.1|GD943045
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|207790357|gb|GD760374.1|GD760374
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|193584350|gb|FK539868.1|FK539868
EST:     CCATCGACGTTGATATTCTGACACTTGGTCAANATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: CCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|207720220|gb|GD703979.1|GD703979
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
EST: gi|192312746|gb|FK003972.1|FK003972
EST:     ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAG                         CCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT
genomic: ATTTAAGGGCCATCGACGTTGATATTCTGACACTTGGTCAATATTTGCAGgtttgttaat ... attgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgatcgtttacttgtggcttattgttaattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA
                          tgttaat  putative branch site (score: 3)
                                         ttttatt  putative PPT
                                    aaagattttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctcagctgataatagtcataatagaccttgcaggtctttattattgatcgtttacttgtggcttattgttaattcgaaagattttattgttgcagCCAACTCCCTTGCACTTAACTGTCAAAGAGTATGTTACTCCTGAGAAGTTTGATTTCTGGAAAGAATATGGGGAATCTATTGGTTTTCGTTACGTAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - -cagctga
- - - - - - - - - - - - - - - ccttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggctt