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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accttatatctcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG

Basic information

species Glycine max
transcript GLYMA02G03080.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 1
accttatatctcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagt--ttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
      |   | |  | |       | |   |  | | |   |  |||  | || || ||  |||  | |||  |  |   |  | |  ||   |  || |||||||||||| || || |||||||| || || ||||| ||||| || || |||||||| ||||| |||||||| ||||||
-----gtgagttcctgtgccgcttttgggaatcatgattgcatcgtgatatctgcttgttcatttgatgtgatatgatcttgattcgatttcccttgtgcagATGGGATGGGAACCGCTGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACAAGCGTGGTGATTATGTGCCTGGATTGAAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 1
-----accttatatc--tcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
       | |  |||  | |  |      |||||   | ||  |  | |  |||   ||  |  |      | |   |   | || || |||  ||   |  | ||||||| ||||| || ||||| ||||| || || |||||||||||||| || |||||||| || || |||||||| ||||||
gtgagttcgtgcatcagttccgggaaacggggttacatcgtgaaaatctgattg---ttcatcatgagaaatatgacgtgatctgggt-ttgatttctgttgtatagATGGTATGGGAACAGCGGAATGGAGGGCAGCGAAGAGTCCTGCTTACTACAAGCGTGGCGACTATGTGCCTGGATTGAAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 1
-----accttatatc--tcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
       | |  |||  | |  |      ||||||  |||   |  |   | ||| ||   || |      | |   |  || || || |  ||||  ||  | ||||||||||||| || ||||||||||| || || ||||| ||||| || || |||||||| || || |||||||| ||||||
gtgagttcgtgcatcaattccgggaatcggggttggattg---agataaatctga-ttacattatgacaaatataacgtggtctgggttt--gattcttttgtatagATGGGATGGGAACAGCGGAGTGGAGGGCAGCAAAGAGCCCTGCCTACTACAAGCGTGGCGACTATGTGCCTGGATTGAAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 1
---------------accttatatctcctagagtga-agggttgtgttgtt--tacttgtttttgaatttt--gttttttttttttttttgaagtttgagtattggat---tggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
               ||| | |   |  |    ||  || | |||| |  |  |  |  |   ||   ||      |      |    | |  |  ||| | | |  |   ||||  ||| ||||||||||||||| || |||||||| ||  ||||||| || ||||| || ||||| ||||| || ||||||||||| |||
gtgagttcttctgttaccatgtgcttggtcagctggtagtgctgtgatagtactgttcatcggtgggattccgaaatcgagagtgggctagtggagtgactttggagtacctggtgtatgcagATGGGATGGGGACGGCAGAGTGGAGGGCCTCCAAGAGCCCGGCTTACTACAAGCGCGGGGACTATGTGCCTGGCTTAAAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 1
accttatatctcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagta--ttggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
                | ||| || || | | ||  | |||   | |   |  ||| | |   ||   ||||  ||  | |   ||| | |  ||   | |||||||||||| || || ||||||||||| ||||||||||| || ||||| ||||| ||||| || || ||||| ||||||
----------gtaagaaatgagggattctatagt--aattggaatcgggct--gttgtgtgagttcgattgagtttcaatttctttgaacttcttttggcagATGGGATGGGTACGGCTGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGCGGGGACTATGTTCCTGGTTTGAAG

upper sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 1
accttatatctcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
                 || |    |   |   ||||  |  ||  |||||  ||  || | |   |||  ||||||     ||| | |  |    | |||||| ||||| || || ||||||||||| ||||||||||| || ||||| ||||||||||| || |||||||| ||||||
-----------------gtaagaaatgagggattttatataattg-gaattgggtggttgtgtgagttt--aagttta---tttgaacttttatgggcagATGGAATGGGTACGGCAGAGTGGAGAGCAGCCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG

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|254335197|gb|GR846694.1|GR846694
EST:     CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACT                         ATGGGATGGGGACTGCGGAGTGGAGAGCTGCCA
genomic: CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACTgtaagtcagt ... gttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCA
EST: gi|51338002|gb|CO981868.1|CO981868
EST:     GCGAGAATAATCACT                         ATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
genomic: GCGAGAATAATCACTgtaagtcagt ... gttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
EST: gi|254322999|gb|GR839912.1|GR839912
EST:     CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACT                         ATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
genomic: CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACTgtaagtcagt ... gttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
EST: gi|15664218|gb|BI701589.1|BI701589
EST:     CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACT                         ATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
genomic: CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACTgtaagtcagt ... gttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
EST: gi|19054086|gb|BM732753.1|BM732753
EST:     CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACT                         ATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
genomic: CGCCGCGCTTTGGGATCTTCCTGCTATTTTGGTCTGCGAGAATAATCACTgtaagtcagt ... gttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
EST: gi|58016174|gb|CX702916.1|CX702916
EST:     TGCGAGAATAATCACT                         ATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA
genomic: TGCGAGAATAATCACTgtaagtcagt ... gttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattttgttttttttttttttttgaagtttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG
                                            ggttaat  putative branch site (score: 4)
     tttgtttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accttatatctcctagagtgaagggttgtgttgtttacttgtttttgaattttgttttttttttttttttgaagtttgagtattggattggttaatgtagATGGGATGGGGACTGCGGAGTGGAGAGCTGCCAAGAGTCCTGCTTATTATAAGCGTGGGGATTACGTGCCTGGCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - -ggttgtg