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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaaattaattgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG

Basic information

species Glycine max
transcript GLYMA18G52780.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g01240.t01 (Vitis vinifera), 3'ss of exon 1
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaa-aattaattgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                        |||| |  ||  || |     || ||| |   | | || |  |   ||       || | | | ||  | ||   ||    | | ||| | || | |||||||       || |||||||| ||||| ||||||||||| ||  | |||||||| |||||||||||||||||||| |||||||||||||| ||||||||||||||||| |||||||
------------------------gtatcaaatgaggattctttcta-tgtgaatgtttagtagaatgcttgtattctacagtctgcctttttcttgtattc---agtctgagataactgattgcaatgttatcttctagGCTGGATTTGCAGGAGATGATGCTCCTAGGGCTGTGTTCCCCAGCATTGTAGGTCGTCCCCGTCACACTGGTGTAATGGTTGGCATGGGCCAGAAAGATG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaa-attaattgcaacaa----atatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                                  |  | | |||||   | | |       | ||  |   | |     |    | ||     |||  |   |  ||  |||        || ||          | |  | ||||||| |||||||| ||||||||||| || |||||||| |||  ||| || || || || || ||||| ||||||||||| || |||||||| ||     
----------------------------------tccatttaacttg--ggcgt-------tgggcctggcgtgggccccgcgctgcagcg-cgttgttcgagcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S381_21V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatg-ggaatatcattttacattaatgttacttttgtgaatttgaaaaattaattgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                                   || ||   ||||   |  || | ||| |   || |||  |    ||   |||       |||  | | |   |||     ||  || ||   ||  || | | |||| ||||| || ||||| ||||| || || ||||||||||||||||| || || || ||  | ||||||||||||||||| |||||||| || || || |
----------------------------------ctgcat--tcttagatttgtagt-ttgctaccttaatgcagtccttcgcgttaggcgtcagttgttgtggaagattgatccaa--aaatggtgcatgtaat-gcagGCCGGTTTCGCGGGAGACGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaaattaattgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
            |||||||  | | |||| | |  ||   | || |   |   ||  ||       ||||||   | ||| | |   |    ||||       | | ||||   |||| |  |||             ||||||||| |||||||| ||||| || || ||||| || ||||||||||| || || ||  | |||||||| |||||||| || ||||| || || || |
-----------ctcttttgcatctttatt-tataatgggcagacat-tggatgtagactaa-----tttatgatca-atcctctcgaaactgtgtt-------taattttggtgaattgaacgca-------------gGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
gtacatgatggatcttttgtttttgtattatttgttgaataaactta-ctgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaaattaattgca-acaaatatt-tgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                                        || |||| ||  | ||| ||   |  ||||||    |  |||| |  |   | |     | |  || |     |  | ||||  |   |  || || || |||||||||| ||||||||||| ||||| || || |||||||| ||||| || || || ||  | ||||||||||||||||| || ||||| || || || |
----------------------------------------aaccttaacttgcgtaccctcaat--ttttatcatcacttcatctgtctggagttcacatctcttgtaacatgatgagtaatcacgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S198_157V6.3 (Physcomitrella patens), 3'ss of exon 2
--------------gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatac-----tcttgttggttttatggg------------aatatcatttt----acattaatgttacttttgtga----------atttgaaaaatta--attgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
              ||   |||||   | ||||| ||     ||| || ||||    ||| |  | | |      |||      | | |||||              |||| | ||    ||||   || ||  | |||||          |  | |||  ||   ||||     | | | || |||||||||| ||||||||||| ||||| || || |||||||| ||||| || || || ||  | ||||||||||||||||| || ||||| || || || |
gtatgatattaactgt-tttgatgatgcatttgtattctccctatgtgatgaagtggcttgcaataaaatgcagttctaaagcatgtcatgggccaagctgggtcgttatcgtcttcttcacatcg-tggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcatt----ttacattaatgttacttttgtgaatttga--aaaattaattgcaacaaat-atttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                                              | | |||| || |  | |  || |||  ||||  |||    | || | | |  | || |   |||    |      |||||||     |||     | |||||||||| |||||||| ||||| || || ||||| || ||||||||||| || || ||  | |||||||| |||||||| || ||||| || || || |
---------------------------------------------caat-tcatgctataatggcgttcatgataatactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaaatta--attgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                               |  | |   || ||    ||| |  || | ||  |   || |   ||||  | |  ||       |        ||  | |||  ||   ||||     | | | || |||||||||| ||||||||||| ||||| || || |||||||| ||||| || || || ||  | ||||||||||||||||| || ||||| || || || |
------------------------------gtcatgggccaagctgg--gtcgttatcgtcttcttcacatcgtggtatctctgtg-atcggcacaa--------aacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: GLYMA18G52780.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S381_18V6.2 (Physcomitrella patens), 3'ss of exon 2
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgtt-acttttgtgaatttgaaaaattaat-tgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                                 || | || || |  |    |   |||| |  || |       |  |||| ||  |    |||| |      | ||  || |  | |||| ||   ||  || | | |||| ||||| || ||||||||||| || || ||||||||||||||||| || || || ||  | ||||||||||||||||| |||||||| || || || |
---------------------------------gtagtatcaaatctccacaaccgtcttctgtgtct-------aggtcatgttggacctgtgtttaggccaatcaacatgtaggagtaatatggtgcatgtaat-gcagGCCGGTTTCGCGGGAGATGATGCTCCCCGCGCTGTGTTTCCCAGCATCGTCGGACGGCCAAGGCACACTGGTGTGATGGTGGGCATGGGACAGAAGGACG

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|120533525|gb|EH261658.1|EH261658
EST:     CTGAGGATATTCAACCTCTTGTTTGTGACAATGGAACAGGAATGGTTAAG                         GCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTA
genomic: CTGAGGATATTCAACCTCTTGTTTGTGACAATGGAACAGGAATGGTTAAGgtacatgatg ... atatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTA
EST: gi|151400056|gb|EV269870.1|EV269870
EST:     CTGAGGATATTCAACCTCTTGTTTGTGACAATGGAACAGGAATGGTTAAG                         GCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTA
genomic: CTGAGGATATTCAACCTCTTGTTTGTGACAATGGAACAGGAATGGTTAAGgtacatgatg ... atatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTA
EST: gi|15814304|gb|BI786579.1|BI786579
EST:     CTGAGGATATTCAACCTCTTGTTTGTGACAATGGAACAGGAATGGTTAAG                         GCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTA
genomic: CTGAGGATATTCAACCTCTTGTTTGTGACAATGGAACAGGAATGGTTAAGgtacatgatg ... atatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattaatgttacttttgtgaatttgaaaaattaattgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG
                              aattaat  putative branch site (score: 3)
                     aatttgaaaaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgatggatcttttgtttttgtattatttgttgaataaacttactgtcatactcttgttggttttatgggaatatcattttacattaatgttacttttgtgaatttgaaaaattaattgcaacaaatatttgtagGCTGGTTTTGCTGGAGATGATGCCCCACGTGCTGTGTTTCCCAGCATTGTAGGTCGTCCTCGTCACACTGGTGTGATGGTTGGCATGGGCCAAAAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG