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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcactttcttttatatgttgtaagctgagtctggagtagttgtgttacttgtgtagttaattatttgccttcacttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAA

Basic information

species Glycine max
transcript GLYMA13G20780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 4
gtatgcactttcttttatatg-ttgtaagctgagtctggagtagttgtgttacttgtgtagttaattatttgccttcacttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAA
||| || ||   |    ||      | |||     |   |  |       ||  |   |  ||  ||| |      || | | |   |||||||||||||| | || ||||| ||||||||||| |||||||| |||||||| || ||||| |||||||||||||||||      |  || |||||| |
gtaagctctgaatccactaaaaccatgagcaagagcaacaaaaacctgtatatatacttgtttgcttactgtatgccattgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTA

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 3'ss of exon 4
-------------gtatgcactttcttttatatgttgtaagctgagtctggagtagttgt--gttacttgtgtagttaattatttgccttcac-ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAA
              ||   | |        |||||| |         | | |||   |    | |          || ||||||    || |  || ||   |||||||||| ||    || ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| |
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaacactcttgattattattattaatatttattgcagTGGATGCTCCAGATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTA

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 4
-------------gtatgcactttcttttatatgttgtaagctgagtctggagtagttgt--gttacttgtgtagttaattatttgccttcac-ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAA--
              ||   | |        |||||| |         | | |||   |    | |          || ||||||    || |  || ||   |||||||||| ||    || ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| |  
gtaagttcaaaaaatactgagtgctagcattatgttctttatgtgcccagaagttactactagatcacaacactcttgattattattattaatatttattgcagtggatgctccagATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAAT

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G540538_T02 (Zea mays), 3'ss of exon 4
gtatgcact----ttcttttatatgttgtaagctgagtctggagtagttgtgttacttgtgtagtta-----attatttgccttcacttcataat----agTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAA
 ||| |||         |||||   |  |   ||   || ||      |    | | | ||||||||     |||  |||    ||  ||||  |    |||||||||||||| | || ||||| ||||||||||| || ||||| ||||||||||| ||||| ||||| |||||||| ||   |  |  ||  || || |
-tatccacggcgagctctttatcaatattccactccttcaggtccctcttcactgcctctgtagttacatcaatttgttgatgacatgtcattgttttcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAACGCTCAAGCTGCAGGAGTTA

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135132_T01 (Zea mays), 3'ss of exon 4
--------------gtatgcactttcttttatatgttgtaagctgagtctggagtagttgt-gttacttgtgtagttaattatttgccttcacttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAA
                |    | || | | || |  |  |   |||      |  |  ||| ||||| |    ||||   |    || |   |||  |   |||||||||||||| | || ||||| ||||||||||| || ||||| || |||||||| ||||| |||||||||||||| ||   |  |  ||  || || |
aaactgcatcatcgaaacaggccttttataatctactaaaccgtgaacaaccaaaaactgtagttacat---cagtttgatgacggcatgtccttgttttcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTA

upper sequence: GLYMA13G20780.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 2
----------------gtatgcactttcttttatatgttgtaagctg-----agtctggagtagttgtgtta---cttgtgtagttaat---tatttgcctt--cacttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAA
                     || |    || | |  |  ||  ||      ||||  || | |||   | |   | |  | | ||||    ||     | |  || | | |   ||||||||||||||   || |||||  |||||||||| |||||||| || ||||| || ||||| ||||||||||| || ||||| |||   || |||| | |
gtaagctctgaagaaaaaccacaataatattcaaagctattagcctatgaccagtcctgattggttacataaactcataagaaattaaaacataacaatcctgacattacttttcagTGGATGCTTCAAATTCCTGGTGCATCAAGTTACATTGGTTGCATCGGGAAGGATAAGTTTGGTGAGGAGATGAAAAA-AAATGCACAAGCTGCTGGTATTA

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|209708530|gb|BW668141.1|BW668141
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|209710379|gb|BW681278.1|BW681278
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|13311384|gb|BG405035.1|BG405035
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|192324906|gb|FK016092.1|FK016092
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCGG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|12773339|gb|BG238266.1|BG238266
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTTCA-GCACCAGGTGCCACAAGTTTCATAGGTTGCATAGGAAA
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTT-CAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAA
EST: gi|213598835|gb|DB968306.1|DB968306
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|209711575|gb|BW676820.1|BW676820
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|4437142|gb|AI523007.1|AI523007
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|209711086|gb|BW681150.1|BW681150
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|151405346|gb|EV275160.1|EV275160
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|151404672|gb|EV274486.1|EV274486
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGCGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|11687342|gb|BF594982.1|BF594982
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|213611486|gb|DB959196.1|DB959196
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|9987590|gb|BE661698.1|BE661698
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|213597865|gb|DB958246.1|DB958246
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|151405163|gb|EV274977.1|EV274977
EST:     GGAGGTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GGAGGTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|19937792|gb|BQ081423.1|BQ081423
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|298174188|gb|HO017524.1|HO017524
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGC
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGC
EST: gi|12773014|gb|BG237941.1|BG237941
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|14126129|gb|BG790567.1|BG790567
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|213591667|gb|DB969767.1|DB969767
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGACAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|213587888|gb|DB959712.1|DB959712
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|213605470|gb|DB964609.1|DB964609
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|208273170|gb|GE070092.1|GE070092
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
EST: gi|4395913|gb|AI494910.1|AI494910
EST:     GTGCTACTCAGAATTCAATCAGGGTTGCTCAG                         TGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG
genomic: GTGCTACTCAGAATTCAATCAGGGTTGCTCAGgtatgcactt ... ttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggagtagttgtgttacttgtgtagttaattatttgccttcacttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAA
                         agttaat  putative branch site (score: 4)
                                  tttgccttcacttc  putative PPT
                      tgtagttaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcactttcttttatatgttgtaagctgagtctggagtagttgtgttacttgtgtagttaattatttgccttcacttcataatagTGGATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA