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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG

Basic information

species Glycine max
transcript GLYMA07G00630.1
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------catctgtttggttgtcatg-ttccattt-attaaaataattcctgtttactaaaaagaatcttgt-tatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                    |   |  |     | ||| ||  |||| | | | || |   |  |  |  |   |   |  ||   ||   |||| | |  || |  |   |   | ||||||| || ||||||||| ||||||| ||||||||||| ||||| || ||||||||||||||||| || || || || || || ||||| ||||| ||||||
gtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttagGCAGACATTGGTCTTGCTATGGGTATCCAAGGAACAGAAGTAGCTAAAGAAAGCTCAGATATAATTATTCTGGATGACAATTTTGCTTCAGTTGTAAAG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 25
---catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
    |||| |    |  |  |    ||| | || ||| ||    | || |     || || | |  |  |||   |||  |||  | ||    | |||   |||| ||||| ||||| || ||||||||||| |||||||||||||| || || || || |||||||| ||| | || || || |||||||| || || | |
gtttatctctcgactaatgttccatcatgttttgaaagaaacaatcttcatgttcaacaaccataatccagtctttcttatgcaatgctgaacttaat---agGCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------catctgtttggttgtc--atgttccatttattaaaataattcctgtt-tactaaaaagaatcttgttatagttaatctcgtgctttactattttgaatt-ttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                                |||   | || || |   | |  | ||||  ||| | |   | | |   |     | |  ||||    |  | |||||  |     | ||||   | || | |||| |||||||||||||||||||||||||||||||| ||||| || ||||| |||||||| || ||||| || || || || ||| | || || || |||
gtacattcaatttgggagttcatattttaaatgaatacaagaattcaacatgcatgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctcaatcttat----cattattcccacttatcagGCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 25
---------------------------------------------------------------------catctgtttggttgtcatgttccatttattaaaataattcct----gtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                                                      |  |    | |  | || |   |||||   ||  |  |       | |    || ||| |||||    ||||   |   |  || |   | ||        |||| ||||||||||| || |||||||| || |||||||||||||| || || || || |||||||| ||| | || || || || |||||||| || | |
gtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttg------cagGCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 24
catctgtttggttgtcatgttccatttattaaaataat-tcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
             ||  | |  || || |  |  | || |  | | |  |       ||||    | |  | || |  |  |||  |  |||| | | ||||| ||||| ||||| |||||||| ||   ||||||||||||||||||||| || || || || || ||  | || || || ||||| ||||| ||||||
-------------gttctctaacaattctacaggttatgtattatgtgttgtgtgtcatctc--caaatctgatttt-tcttttgttgctttggactatagGCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 26
---catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatctt-gttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
      ||||   |||   |||||   ||| |  |  |    |  ||| |  |    |  |||| || ||  || |||    | | ||  |||||  ||| ||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||| || || ||| | || ||||||||||| ||||| ||||||
ttatggctgtagagtttggatgtt--gtttttccatcttcagcaggttcataatgttgtttctttgtaatgattgatc--aggttgtatcattttctattgtagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: EFJ08462 (Selaginella moellendorffii), 3'ss of exon 22
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                          ||||   ||| |  ||  |    |  | |  |||||| |      || |   || |||||  ||||||| || || ||||| ||   ||| |||||||| ||||| ||||||||||| ||||| || || || ||||||||||| || || || || 
------------------------------------------gtttgagaaatatgatacttcctt--tcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTATAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCGTCGGTTGTCAAA

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 22
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                          ||||      ||  ||| |   |    |  |||  || |  ||| || |       |||||||||| |||||||| |||||||||||||| || || || || |||||||||||||| |||||||| || || || ||||||||||| || || |||
--------------------------------------gtgggtttggcggtaatcatcgtag-acgcattttctgatgataaactgttat------cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: EFJ15121 (Selaginella moellendorffii), 3'ss of exon 20
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                          ||||   ||| |  ||  |    |  | |  |||||| |      || |   || |||||  ||||||| || || ||||| ||   ||| |||||||| ||||| ||||||||||| ||||| || || || ||||||||||||||||| || || 
------------------------------------------gtttgagaaatatgatacttcctt--tcatgctcgtgttgctgatttgtttgttctagGCACATATTGGGCTATCCATGGGAATTGTAGGCACTGAAGTCGCAAAGGAAAGCTCAGACATTATTATTCTGGATGATAACTTTGCATCAGTTGTCAAA

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 24
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatctt-gttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                          ||||      ||  ||| | ||   | ||  |||  || |  ||| || |       |||||||||| |||||||| |||||||||||||| || || || || |||||||||||||| |||||||| || || || ||||||||||| || || |||
--------------------------------------gtgggtttggcggtaatcatcgtagtcgcattt--tctgatgataaactgttat------cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

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|33390180|gb|CA853387.1|CA853387
EST:     TTGTTGCGGTCACAGGAGACGGCACCAATGATGCTCCTGCCCTACATGAG                         GCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAA
genomic: TTGTTGCGGTCACAGGAGACGGCACCAATGATGCTCCTGCCCTACATGAGgtctgtccta ... tgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG
                                       ctatttt  CT-rich tract
                                   tttactattttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctgtttggttgtcatgttccatttattaaaataattcctgtttactaaaaagaatcttgttatagttaatctcgtgctttactattttgaattttagGCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA