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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtgtttatcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgatattatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG

Basic information

species Glycine max
transcript GLYMA10G30400.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 5
atggtgtttatcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgatattatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG
   || |  | | |    | |      | | |           | |   |      | |   ||| ||       || |||| |  |     || | ||| ||||| || || |||||||| |||||||| || |||||||||||||| ||||| |||||||| ||||||||||| || |||||  |||| ||| | | |
---gtatgcagctacttgtcacattattatctagatagaacactaaaccacacctgattagatgagaagctggtctaatatgatacaaacaatt-tctagGTTGACAAAGTCGGACTTCCGTGAGCCAGTGAACATTGGAAGCGATGAAATGGTAAGCATGAACGAGATGGCTGAAATCATTCTCAGCTTCGAGGATAGG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 5
---------------------atggtgttta--tcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgatattatggtctat-tgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG
                     ||  |    |  | |||||| |    || ||||   |   ||   |     | |    ||||     |  | |  |||  |     |  | |||    |  |||||||| || || |||||||| |||||||| || || ||||||||||||||||| |||||||| ||||||||||||||  | || ||||||||| | | |
gtatgtctgtgtgctttggatatactaccaaatttaagcaagagct-agctgttgcctgtgttgtgtatagcaatggagaatcgacattgtatgacgatgatgcccacactgtgtgcactgcagATTGACCAAGTCAGACTTCCGCGAGCCAGTGAACATCGGAAGCGATGAGATGGTGAGCATGAACGAGATGGCTGAGATCGTGCTGGGCTTTGAGGATAGG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 5
atggtgtttatcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgatattatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG
                     ||  | | | |  |  | ||  |||  | || ||| |    | ||    | ||||||| | |||  || | || | ||| ||||| ||||| || ||||| ||||| || || || ||||||||||||||||| |||||||||||||||||||||||  ||||  |||||||| | |||
--------------------gtgagggtatctcctgatgttgatgaagttgtatgttagacgtaattg--gctgatattttcgtcatttttgttttatagGTTGACAAAATCAGATTTCCGTGAGCCGGTGAACATCGGAAGCGATGAGATGGTGAGCATGAATGAGATGGCTGAGATGGTTCTCAGCTTTGAGGAAAAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ12864 (Selaginella moellendorffii), 3'ss of exon 4
atggtgtttatcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgata--ttatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG
                     ||    | ||||     ||||| || ||  |     |||  |  |||| |    |   || |  | | ||||  ||   ||  |||| || || ||||| || || ||  | ||||| ||||| ||||||||||| |||||||| |||||||||||||||||  | || ||||   |||||
--------------------gtgtgtctctttttctgctttctggaattgatggtcgatcgatactaaatgccttttgctttttctttcttgtcgtgcacagGCTGACAAAGTCGGACTTTCGTGAACCGCTCAATATCGGAAGTGATGAGATGGTGAGCATGAACGAGATGGCTGAGATTATCTTGGGTTTTGGAGACAAG

upper sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ09286 (Selaginella moellendorffii), 3'ss of exon 4
atggtgtttatcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgata--ttatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG
                     ||    | ||||     ||||| || ||  |     |||  |  |||| ||   |   || |  | | ||||  ||   ||  |||| || || ||||| || || ||  | ||||| ||||| ||||||||||| |||||||| |||||||||||||||||  | || ||||   |||||
--------------------gtgtgtctctttttctgctttctggaattgatggtcgatcgattctaaatgtcttttgctttttctttcttgtcgtgcacagGCTGACAAAGTCGGACTTTCGTGAACCGCTCAATATCGGAAGTGATGAGATGGTGAGCATGAACGAGATGGCTGAGATTATCTTGGGTTTTGGAGACAAG

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|6847778|gb|AW350068.1|AW350068
EST:     CAAACACGATCATTNNNNNTCATTGATGAGTGTGTTGNAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATANTNNNAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|21594289|gb|BQ610114.1|BQ610114
EST:     GTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: GTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|20813910|gb|BQ298388.1|BQ298388
EST:     CACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|13311333|gb|BG404984.1|BG404984
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|192294959|gb|FG986678.1|FG986678
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|58018643|gb|CX705385.1|CX705385
EST:     GTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: GTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|20813404|gb|BQ297882.1|BQ297882
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGA
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGA
EST: gi|298176590|gb|HO023177.1|HO023177
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|8669973|gb|BE191080.1|BE191080
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|4290524|gb|AI438086.1|AI438086
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|120528817|gb|EH256951.1|EH256951
EST:     CATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|298191001|gb|HO038480.1|HO038480
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCCTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|7587929|gb|AW703735.1|AW703735
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|6502418|gb|AW203791.1|AW203791
EST:     CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
EST: gi|6846118|gb|AW348408.1|AW348408
EST:     CAAACACGATCATTTNNNNTCATTGATGAGTGTGTTGAAGGTGTGCTTAG                         ATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT
genomic: CAAACACGATCATTTACCTTCATTGATGAGTGTGTTGAAGGTGTGCTTAGgtatgtcttg ... ttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttagtttgtaatctttgataaaagttgatattatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG
                        agttgat  putative branch site (score: 5)
                                             ttttgttt  putative PPT
               tttgataaaagttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtgtttatcaagcaataatggagatgttttatccttttcttgagttagtttgtaatctttgataaaagttgatattatggtctattgttttgtttagATTGACTAAATCTGACTTCCGAGAGCCAGTAAATATTGGAAGCGATGAGATGGTTAGCATGAATGAGATGGCTGAGATTATTCTTGGCTTTGAGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG