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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaaatggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT

Basic information

species Glycine max
transcript GLYMA06G16440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 2
ttttgattagaaaaggattagaattgc-ataagttttgatctttca--gtttttttttatttttataaaaat---ggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCG-CACCGAAGATGAATCTTGAAATGATTCATAGTT-
        | |||    |||  |   | |   |  |  ||    ||    | ||  | | |||  ||| |||    | | |  ||||| |   || |  |   ||| | ||||||||||||||||| ||||||||||||||||| ||   ||| ||||  ||| |||||   | | |||  || ||  | ||||          |   
------ccaaaaactttttaccaccaccactcgcatgcattccacatcaatcttgatcactttgctaataatttcagttttttttttggttaatttttttttgcagTTGGATGATTGGGTGTTGTGCCGAATCTACAACAAGAAGGGAGTGATCGAGAGGTACGACACGGTGGACGCCGGCGAGGA--CGTGAAGCCGGCGGCGGCGG

upper sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaaatggatctgatttt-gttgtgttatggtgc-acagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT---
  || ||| |       | |  ||    | | | |||   |  |    |  | |  | || || ||| | ||| ||||||| | ||  || || |    ||||| |||||||||||  |||| ||||||||||||||||||||     | |||||    | |  | | ||  ||  |  |||  ||  ||| ||    ||     
--ttaattgggcggatttcatcatatatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGC--GGCGGCGGCGGCGGCGAACGTTCGAAT-ATGATGAGCCACG

upper sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 2
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttat---ttttataaaaatggatctgattttg--ttgtgttatggtgc-acagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCG-CACCGAAGATGAATCTTGAAATGATTCATAGTT
     ||   | ||   ||  |  |   |    || |||   |   |||  |  |||     | || || ||   | |  | | |  || | || || ||   ||| | |||||||||||| |||| ||||||||||||||||||||   | | |||||    | |    ||| |  |   |  ||  |  | |   |      |  
---aaatcgtataattgttctacctttttg---ttggatggatagatttggtggtatgggcgtgattaagatttttttcctctcggttttttttttgctgttgcagTTGGATGATTGGGTGCTGTGCCGAATCTACAACAAGAAAGGCGCGCTGGAGAAGCCGACCGGAGCCGGCGGCAGGGCCGAGGCCAGCAGCCAGGGCGCGC-

upper sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaaatggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT
       ||      | ||   |||   | |  | | ||||||  ||   |  | ||||  || |   |  |  |  || || || ||| || || |||||||||||||||||| || |||||||| |||||||||||||| |  || ||||| ||   | |  | |    ||||  ||        |  ||   |    
------gtaagttctgtttcttattaacttatgtatcatcttttcgtgaatgatgatttagatta---ttaactttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC

upper sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 2
ttttgattagaaaaggattagaat-tgcataagttttgatctttcagtttttttttatttttataaaaatggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT
 |  | ||     |   |||   | ||  |   ||||    |||     |  |  |   || || |  ||  ||  | |||| |||  | |   |   ||||||||||||||||| |||||||| || ||||| |||||||| |  || ||||| ||     || | ||  |  |||        |||| |||   ||  |
gtaagcttttctgatttttaatttctgggttttttttcgatttttgtgatgatgatgaattgatgatgattaatgggttttttttggttgaaattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAGAAGTATTTACCGGCGGCGGCTGAGAAACCGACGGAAAAGATGAGTACGT

upper sequence: GLYMA06G16440.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 2
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaa--atggatctgatt-ttgttgtgt-----tatgg--tgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT-----
 |  ||||  ||    || |  |    | |  | || || | | | ||       |     | | |   |||| |||  || ||| | | |     ||| |  |   |||||||| |||||||| || |||||||| |||||||||||||| |     |||||| |  ||||    | | | ||  | |||   ||||| || || |  |     
gtacgattgtaattctat-actacattaaagatatttatttattatttaaaaaaaaaagaaaaagagtgatggttctttttattgatatatattattattgactttgcagCTTGACGATTGGGTCTTATGTCGAATATACAACAAGAAAGGCAGCGCCGAGAAACAGCACACCTTTG-ATCAAAAGTCAAT---GAAAT-ATCCAGAACTTGAAG

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|151408244|gb|EV278052.1|EV278052
EST:     TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGG                         CTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
genomic: TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGGgtatgtccca ... tggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
EST: gi|21677597|gb|BQ629948.1|BQ629948
EST:     TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGG                         CTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
genomic: TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGGgtatgtccca ... tggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
EST: gi|24135371|gb|BU925890.1|BU925890
EST:     TCGCCAATGTTGACCGATCTGCCTCCAAGAAAACCAACAACAACTTGAGG                         CTTGATGATTGGGTGTTGTGTCGAATCTACCACAAGAAAGGGAAGATTGAG
genomic: TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGGgtatgtccca ... tggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
EST: gi|151408153|gb|EV277961.1|EV277961
EST:     TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGG                         CTTGATGATTGGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGA
genomic: TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGGgtatgtccca ... tggtgcacagCTTGATGATTGGG-TGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGA
EST: gi|23053535|gb|BU577577.1|BU577577
EST:     TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGG                         CTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
genomic: TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAACAACAACAACTTGAGGgtatgtccca ... tggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttttttatttttataaaaatggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT
                          atctgat  putative branch site (score: 4)
     tttttatttttataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgattagaaaaggattagaattgcataagttttgatctttcagtttttttttatttttataaaaatggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACGACCGCACCGAAGATGAATCTTGAAATGATTCATAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG