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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaataatcttctattgagttgagttgaatcagtgttttgattctgcgtgttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA

Basic information

species Glycine max
transcript GLYMA07G39380.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 2
gtaaagaataatcttctattgagttgagttgaatcagtgttttgattctgc--gtgttgcgtaggtttatgtggttttgtt--ttaatttgaacgtttgattttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA
           |  | |   | ||||   ||||  |  |  | |   ||     | |   || | |  |  |   ||| ||  | ||||||   |  |  | | ||    |||||||||||| ||   |||| |||||  |    ||||||| |||| ||| |||||||||||  ||||||||||||| |||||||| || ||  | || ||
----------gttgtgtcccg-gttgcactgaaaaatcgaataggcactaatgatatattgtggttccaaatatatttcttgatgaatttgcttgccttgtgtcggacc-agATTACCTGCAGGAATATGCAAAAGGATCCGTCATGTATGGATTCAAGGGAGGTCCAGCTGGAGTCATGAAGTGCAAGTACGTTGAGCTCACTGCGGATTA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 2
gtaaagaataatcttctattgagttga-gttgaatcagtgttttgattctgcgtgttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA
        |    | | ||||||| ||   ||||  ||| |   | || ||   | |     |    |  |  || | ||| | ||||   | |     |||| |  ||| || || || || | |||| |||| ||||| |||||||| || | ||| || |||||||| |||||||||||||| || || ||||| || ||||||| 
-------tttgcatacaattgagtagacagtgaaagagtttgacggttttgaaggctttcctgaaaca-attattgtctttgactttgtttggtgtgcgttggatc-agACTATCTACAGGAGCGTGCAAAAGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTT

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaagaataatcttctattgagttgagttgaatcagtgttttgattctgcgtgttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttgg--ttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA
|||| |  |    || ||         ||  ||| | ||||||  || |   | |||   |    |   ||   |||||  | | |  |  |||| ||| ||  | ||||||||||||||||| | |||  |||| |||||||| || || |||| ||||||||||||||| |||||||| |||||||| |||||  | |   | || ||
gtaagggtttgatttttac--------gtcaaatga-tgtttttttttttttttttgtagaatagttgctgacattgttccactcttgat-tttgttttcggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA

upper sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 2
gtaaagaataatcttctattgagttgagttgaatcagtgttttgattctgcgtgttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA
|| | ||   ||  || |   | |||  |    |  |  |||   |  ||  || || | |  ||  |  |      |  | ||||   |||||| | | |||   ||||||  ||||  | | ||   ||||||||||| ||||||| |||| ||||||||| ||||| ||||||||||||||||| ||||||||   ||| || | 
gtgaggatcgat--tcgacatatttggatcttgtgtgattttgactcttgtttgatgtggaaattcgttgga----ataatgattttt-cgtttgttgtcggt---agATTATTTGCAGAATCATGTGAAAGGAAGCACACTGTATGGGTTCAAGGGTGGTCCCGCTGGGATCATGAAGTGCAAATATGTTGAACTCGACTCTGAATT

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|254318249|gb|GR832417.1|GR832417
EST:     GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCG                         ATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
genomic: GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCGgtaaagaata ... ttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
EST: gi|7591049|gb|AW706790.1|AW706790
EST:     GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCG                         ATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
genomic: GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCGgtaaagaata ... ttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
EST: gi|207700556|gb|GD683663.1|GD683663
EST:     GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCG                         ATTACCTGCAAGACCTTGCAGAA
genomic: GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCGgtaaagaata ... ttggttttagATTACCTGCAAGACCTTGCAGAA
EST: gi|193585833|gb|FK541233.1|FK541233
EST:     GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCG                         ATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
genomic: GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCGgtaaagaata ... ttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
EST: gi|254323780|gb|GR836119.1|GR836119
EST:     GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCG                         ATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
genomic: GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCGgtaaagaata ... ttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
EST: gi|213599182|gb|DB958401.1|DB958401
EST:     GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCG                         ATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG
genomic: GTCCGGTGGCCAGGCTCCCGGCGGTCACAATGTTATTTCTGGAATCTTCGgtaaagaata ... ttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA
                   ttttgttttaatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagaataatcttctattgagttgagttgaatcagtgttttgattctgcgtgttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttggttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG