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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

Basic information

species Glycine max
transcript GLYMA07G38050.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttttattattttgttgcaag-attgatggatta-tataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
            |  |||||  ||   | | | |||| ||   | | | ||| ||| | || ||  | ||||    || |  || |   | ||||||| ||||| |||||  || | |||||||| ||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||| | ||
-----------gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttt-tattattttgttgcaagattgatggattatataacatggtacaatctatttgtgta----tgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
               |||   | |||| ||  ||  || ||| |  |  | |||    | | | | ||    |   |||  |   ||     | ||||||| ||||| |||||| |  | || ||||| |||||||||||||||||||| || || |||||||| || ||||| |||||||| ||||||||| | ||
---------------gttagttttttgcttcataaaatgttgcttgacaaatgaaaattcaaacatcaattaatgttcttctgtcgtggtgtttcagCTGTCAATAAGGATGAGCTATTGCAGATGGTCAGATTTGGTGCTGAAATGGTATTCAGCTCCAAGGATAGCACAATAACAGATGAAGATATTGACCGCAT

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
gtaagggttt----tctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
||| || |||    | ||   ||| | |||||||| |  ||||| || | || |||||    |  ||      | ||||  |  |  | |||  |||||| ||||| |||||  | || ||||||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
gtatggttttgatatttgccatttctatttgttttaagcatttt-ttactagtttgat---ctggattgttctg-acaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
-----gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggt-acaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
     || | | | || ||  |||  | |||||||  |  |||||  |  |    |  | |  |||  |  ||  | ||||  |  || | | |  |||||| ||||| |||||  | || ||||||||  | |||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||| | ||
gtatggttatgatatt-tgcctttgctatttgtttcaagcatttttcttta---ctagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
             |    |    | |    | |||  ||| |     | || ||   | | | ||  |||||   |    ||   ||||||||||| ||||| |||||||||||||||||||| |||| ||||||||| ||||| || ||||| || || || ||||| ||||| ||||||||||| |||||
-------------gtaagtgcgttatacagtgattgctttatgcattggttcatctctgacagaat-tggtat--ttatcttaactatgcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
||||| | ||       | ||     | | |||    | | ||| |   |   |    ||||||   || |    | | ||||  | | ||||||| ||||| |||||||||||||||||||| |||| ||||||||||||||| |||||||| || || || |||||||| ||||||||||||||||||||
gtaagtgcttg------tgtactgaggctgtta--gatgtattggattttctcttacatatatatactgatttcttttctttgc-tttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
gtaagggttttctgggttttatctttgtttt-tattattttgttgcaagattgatggattata-----taacatggtacaatctatttgtg--tatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
|| ||   ||||||  ||  |   ||| |||  | |||    | || |  |    | | || |     ||||||  |    | | | || |  | ||||||||| || ||||||||| | || |||||||| || |||||||||||||||||||| || |||||||| || |||||||| ||||| || || ||||| ||
gtgagccatttctgcattacaagcttgctttgcactatgacat-gctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT
                      atataac  putative branch site (score: 3)
                   attatataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggttttctgggttttatctttgtttttattattttgttgcaagattgatggattatataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT