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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagattaagatattttcgtatattctaacacaagtatttagcatactggtttctctagtttatttacactgtaatggtttgaattgaattgttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

Basic information

species Glycine max
transcript GLYMA10G02410.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
aagattaagatattttcg--tatattctaacacaagtat-ttagcatactggtttctctagtttatttacactgtaatggtttgaattgaattgtt--ttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
        | || | ||      ||  ||   |||  || ||| ||||||        | |  |  | ||| ||   |  | | || | | || ||  |||  ||||||| || || ||||| |||||||||||||  || ||  | |||||||| ||||| | ||| ||||| ||||| ||||||||||||||||| || ||||
--------gttactctccatctcatcatattgcaaacatattatcatactcacacagttggaat-ctcacagtgctttactcttaaattactttttccttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA

upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
aagattaagatattttcgtatattctaacacaagtatttagc-atactggtttctctagtttatttacactgtaatggtttgaattgaattgttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                    || |   | | || | ||  || ||  ||  | |         | |  | | |||   ||   || |   | || |  |||||||| ||||| ||||||||||| ||||||||||||||  | || || ||||| || | |||||| || ||  | ||   ||||||||| ||||| ||||
-------------------gtaattatatagaaatcttatgctattttgactccaaattaacttctggattttaacaattattat-gctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA

upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 19
aagattaagatattttcgtatattctaacacaagtatttagcatactggtttctctagtttatttacactgtaatggtttgaattgaattgttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
               |  |||  | | ||  || | | |  | | |     |  |||||   ||       | | |  |||  ||    |  | |  |||||||| ||||||||||| |||||||||||||||||  |  | ||||| |||||||| |  ||||| || ||  | |||||||||||||||||| | ||||
--------------gtaatattatgttacttaa-tttctttcttcccaagctgcctagtaagttccgg--attaagagttggtttactatactgtttcagGATGTTGTTACTGAGAACGAATTTGAGAAAAAACTGTTGTCGGATGTCATTCCACCTAGCGATATAGGTGTTTCCTTTGATGATATTGGAGCTCTGGAAA

upper sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
---aagattaagatattttcgtatattc-taacacaagtatttagca-------tactggtttctctagtttat----ttacactgtaatg-gtttgaattgaattgt-----tttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
   ||| |  |||| | |   || |||| |  | | | | | ||  |        ||   ||  || ||| |||    |||     | |   ||| |||||    ||      |||  |||||||||||||||||||||||||||||||| ||||| ||| | |||||||||||||| | ||||||||| || || |||||||||||||||||||||||||
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA

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|16279857|gb|BI943651.1|BI943651
EST:     TTCTACAGGGCATTCAAAATGAGAACAAGAACATGAAAAAATCACTTAAG                         GATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATT
genomic: TTCTACAGGGCATTCAAAATGAGAACAAGAACATGAAAAAATCACTTAAGgtaatttaac ... gttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATT
EST: gi|193356614|gb|FK321885.1|FK321885
EST:     TTCTACAGGGCATTCAAAATGAGAACAAGAACATGAAAAAATCACTTAAG                         GACGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATT
genomic: TTCTACAGGGCATTCAAAATGAGAACAAGAACATGAAAAAATCACTTAAGgtaatttaac ... gttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtttctctagtttatttacactgtaatggtttgaattgaattgttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA
                                           ttgttttccc  CT-rich tract
                                    aattgaattgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagattaagatattttcgtatattctaacacaagtatttagcatactggtttctctagtttatttacactgtaatggtttgaattgaattgttttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - ctaacac
- - - - - - - - - - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtttg