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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctagacttctacaatattttgctatgtgagggtgagttttggaagtttttgaatgacactgccaacaacctgtcatatgctatgcttttatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG

Basic information

species Glycine max
transcript GLYMA17G17790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10940.1 (Oryza sativa), 3'ss of exon 4
tcctagacttctacaatattttgctatgtgagggtgagttttggaagtttttgaat--gacactgccaacaacctgtcatatgcta---tgcttttatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG
    ||  || ||  | ||||     | | ||       | |     || ||  ||  || | ||   | |   |   || ||| |   |  |||  ||   ||||||||| || || |||||| | || ||||| || |||   ||||||||||| |||||||||||||| |||||||| |||||||||||||||
---cagtgttatagcaaatttattggttttagaagactatataagttttcttatatttgaaaatgtggatagttt--tatctgcaaacttattttctttatccagATACTTCAAAGGGCCTGAATTGCTGGTTGACTTCCAAAGTTATGACTACTCTTTAGACATGTGGAGCCTTGGCTGTATGTTTGCTGGAATG

upper sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 3'ss of exon 4
--------tcctagacttctacaatattttgctatgtgagggtgagttttggaagtttttgaatgacactgccaacaacctgtcatatgctatgcttttatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG
        || | || ||||  ||| ||||    |  || ||    |  |   | ||       ||   |  |   ||  | | |  | |  | | ||  || ||||||||||||||||| || |||||||| |||||||| ||||| ||||| || || || || |||||||| ||||| ||||||||||| ||||||
tgtggttttctttgatttctgaaat-ttttatagtaagatgggagatcctaagaattca-----gattttttcg-taaggtttgaagttcctttcctt-gttactcagATACTTTAAGGGGCCAGAACTTCTTGTTGATTTGCAAGATTATGATTATTCTTTGGATATGTGGAGCCTTGGTTGCATGTTTGCGGGAATG

upper sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 3'ss of exon 4
tcctagacttctacaatat---tttgctatgtgagggtgagt--tttggaagtttttgaatgacactgccaacaacctgtcatatgctatgcttttatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG
        ||||| |  ||    ||| | |||  |  | | |   |||   | | |  |   |   | | |  |   |   || |||        | |    ||||||||||||||| ||||||||||| |||||||| |||||||||||||| || || || |||||||| || || || |||||||| ||||||
-----attttctatagcatagacttgatttgtttgtataaatatcttgcttgctgtataggcaattttctaggatgttaatatttgcatgttccctgtaatccagATACTTTAAGGGGCCTGAACTTCTTGTTGATTTGCAAGACTATGACTATTCTTTGGATATGTGGAGCCTAGGTTGTATGTTTGCGGGAATG

upper sequence: GLYMA17G17790.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 3'ss of exon 4
tcctagacttctacaatattttgctatgtgagggtgagttttggaa-gtttttgaatgacactgccaacaacctgtcatatgctatgctttt--atttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG
       ||  ||  || ||  |   |       | ||| | |  | || ||| |  ||  ||        |   |    |||  ||  | |   | | | || |||||||||||||| ||  | || || ||| | |||||||| || || || || |||||||||||| | || ||||||||||||||||||
---ggttctattatgattttaagtacttgttccctcagtgtcgtcacgtctttcagggatgctagtttttgctcatatattgcagtgtctcttcgtgtattagGTACTTTAAGGGCCCAGAGTTACTTGTCGATCTTCAAGACTACGATTATTCTTTGGACATGTGGAGTTTAGGATGCATGTTTGCTGGAATG

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|15285633|gb|BI469524.1|BI469524
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|10238106|gb|BE806994.1|BE806994
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|193642120|gb|FK587164.1|FK587164
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|10238225|gb|BE807113.1|BE807113
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|16345458|gb|BI971053.1|BI971053
EST:     ATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTAAAGGGCCCTGAACTTCTAGTTGA-TTACAAGACTATGACTACTC
genomic: ATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|15000106|gb|BI320920.1|BI320920
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|16283183|gb|BI945415.1|BI945415
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|151412099|gb|EV281911.1|EV281911
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|58018593|gb|CX705335.1|CX705335
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTC
EST: gi|193339637|gb|FK304886.1|FK304886
EST:     GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAG                         ATGCTTTAAGGGCCCTAGAAACTTCTAGTTGATTT
genomic: GCTGAATTTTATCATCCTGGAAAGGAATACAATGTTCGTGTGGCTTCAAGgtaatgttct ... tatttctcagATACTTTAAGGGCCCT-GAA-CTTCTAGTTGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttttgaatgacactgccaacaacctgtcatatgctatgcttttatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG
                                       tgcttttatttctc  CT-rich tract
                                          ttttatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctagacttctacaatattttgctatgtgagggtgagttttggaagtttttgaatgacactgccaacaacctgtcatatgctatgcttttatttctcagATACTTTAAGGGCCCTGAACTTCTAGTTGATTTACAAGACTATGACTACTCATTAGACATGTGGAGTCTTGGCTGCATGTTTGCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - -cttctac
- - - - - - - - - - -tgctatg
- - - - - - - - - - - - - - - -gggtgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgct