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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttttcaactctttttttagtttagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT

Basic information

species Glycine max
transcript GLYMA05G36930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g12150.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------gtaagcttttcaa---ctctttttttagtttagtttagtt-tctcactttcctcacccaaattcag---gttacaaattattg-atgttaaattata---cagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
                                       | |     ||||   |  | | || | |||  |   |   | | |           | |||  ||     | |||||  |||  | ||   || |    ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || |||||||| || || || |||||||||||||||||  | || |
gtatgcaccattctaccttcaaatctttgatcaaaaccatgatgccatcaatggcattgtgttcaatttgttcaggagatatgatgagttgggttctaatggagtgcaatgcaaatgtttgtgtttttgtttgtctttcagGTTGATCTTGTTGGAGGTTATTATGATGCAGGGGACAATGTCAAGTTTGGGTTGCCAATGGCGTTCACGGTGACCATGATGTCGTGGAGCATATTAGAGT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g12070.1 (Oryza sativa), 3'ss of exon 1
----gta-agcttttcaactctttttttagtttagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
    ||  ||   |||| |  ||| |    | | |  | |         |||  || |   || ||  | |    ||  |  | ||   || | ||||||||||| ||||| |||||||| || || || ||||| || ||||||||| | || |||||||| || || || |||||| |||||||| |||| || |
gtacgtggagtcgttcaccattttctccgttcttgaattgcaggatgtgttctacagctccatgcatctgatctgttgattttttttcttttttcagGTGGATCTTGTTGGTGGGTACTACGACGCCGGCGACAACGTCAAGTTCGGGCTGCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCATCGAGT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g12030.1 (Oryza sativa), 3'ss of exon 1
----------------------------gtaagcttttcaactctttttttagtttagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
                            | || | |   | || | | |    || |  ||  |   |    ||       |||   |  |||  |   ||   || |  | ||   ||||||||||| ||||| || ||||| || || || ||||| || ||||||||||| || |||||||| || || || |||||| |||||||| || | || |
gtacgtgctcccgccattgtggcagctagcaaacctgcaatctttctctgctcttgatcttgatcagtacggtttaatttgcaagaacgtgttctattctacacatctacattt---cagGTGGATCTTGTTGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCCTCGAGT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143747_T01 (Zea mays), 3'ss of exon 1
-----------------------------gtaagcttttcaactctttttttagtttagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaatt-----atacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
                              | |||     | |  | |    |    || |  |||  || || | || | |   |||   |||     |  || |||||   |        ||||||||| || || ||||||||||| || ||||| ||||| |||||||||||  | ||||||||||| || || || |||||||||||| ||||| | || |
gtatgcacaacgcgtctctcgttgcattaattagcaagcaagcattgtgaccatggcagctgggttcgtcgctgtgctgaacacgatttttgttttggttcttttatgttttgtctcgccggacagGTGGACCTCGTCGGAGGGTACTACGACGCAGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGGTGACCATGATGTCGTGGGGCATCCTGGAGT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G11050.1 (Arabidopsis thaliana), 3'ss of exon 1
--------gtaagcttttcaact--ctttttttagtttagtttagtttctcactttcc-tcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
         ||| | |   ||    ||  ||||  |   ||||| ||  |     | | | |     |||    ||||  ||| | ||    || ||   |||||||||||||| ||||| || ||||| || || ||||||||||| |||||| | || ||||| || || || || |  ||||  ||||||||||| ||||
ttggccacctaaacgtcaaaaggagctgatttttataacgtttaattaatagtactacattatgtttattttaattac--attttcga-aaaaatttgagcagGTGGATCTAGTGGGAGGATATTATGACGCCGGAGACAATGTGAAATTCGGGCTTCCGATGGCTTTCACGGTGACAACAATGTGTTGGAGCATCATAGAAT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0025g01380.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtaagcttttcaactctttttttagtt-tagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
                                     ||||   |             | || || || | ||  ||  |     ||      || | |||      |||     || | ||||  |||||||||| || ||||| || ||||||||||| |||||||||||||| ||  |||||||||| || |||||||| |||||||| ||||||||  | || |
gtaagttcattttccactccaactcaaaatttctgaaaagcccattgtggaacaagacaattataattgaattattccatacaaccaaatgtgttgaagttttttgctataatctttgagttatgtagGTGGATCTGGTGGGAGGATATTATGATGCAGGTGACAATGTGAAGTTTGGCCTACCCATGGCATTCACCGTTACAATGATGTCATGGAGCATAGTGGAGT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ12750 (Selaginella moellendorffii), 3'ss of exon 1
-------gtaagcttttcaactctttttttagtttagtttagtttctc--actttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
       |     ||      | | |||    ||  | |  |  | |   | ||   |        ||  ||| |   ||  | |   |  || ||  ||||||||| | ||||||||||| || || || || |||||||| ||||| ||  | |||||||| || ||| | || |||||||||||||||  ||| || |
atagatagctgcattcgaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactac-cagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGCCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT

upper sequence: GLYMA05G36930.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ13916 (Selaginella moellendorffii), 3'ss of exon 1
-------gtaagcttttcaactctttttttagtttagtttagtttctc--actttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
       |     || |    | | |||    ||  | |  |  | |   | ||   |        ||  ||| |   ||  | |   |  || ||  ||||||||| | ||||||||||| || || || || |||||||| ||||| ||  | |||||||| || ||| | || |||||||||||||||  ||| || |
gtagatagctgcattctaggatatctttccctttcggatgtgcctttgcgaattgagtactttgcgttgtggtgattgatggtggcgctggaactac-cagGTGGATTTGGTTGGAGGGTATTACGACGCGGGCGACAATGTCAAGTTTGGTCTGCCCATGGCCTTCACCATCACCATGATGTCGTGGAGCGCCATCGAGT

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|213604734|gb|DB956089.1|DB956089
EST:     GAGTCACATGGAGAGCACATTCTGGTTTGCAAGATGGCAAAGCAAGCGGG                         GTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGG
genomic: GAGTCACATGGAGAGCACATTCTGGTTTGCAAGATGGCAAAGCAAGCGGGgtaagctttt ... aattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGG
EST: gi|24135951|gb|BU926461.1|BU926461
EST:     GAGTCACATGGAGAGCACATTCTGGTTTGCAAGATGGCAAAGCAAGCGGG                         GTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGG
genomic: GAGTCACATGGAGAGCACATTCTGGTTTGCAAGATGGCAAAGCAAGCGGGgtaagctttt ... aattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcactttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT
                          ttacaaattattgatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttttcaactctttttttagtttagtttagtttctcactttcctcacccaaattcaggttacaaattattgatgttaaattatacagGTGGATCTAGTTGGAGGGTACTATGATGCAGGGGACAATGTGAAGTTCGGGTTACCCATGGCGTTTACCGTTACGATGATGTCGTGGAGCATCATTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA