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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

Basic information

species Glycine max
transcript GLYMA08G09180.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g08280.1 (Oryza sativa), 3'ss of exon 6
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA
                                              ||| |  |   || |  |||  ||  |  || |  |        || |   |   |   | ||          |||||||| |||||| |||| || ||||| ||||||||||||||||||||||| || ||  |  |  |||| || || || || || |||||||| || ||||
---------------------------------------------gtttgtcctgaattattctttgcctagtacaggtccacgagagttacttgggtaatctggtgtttgaatgctggcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATACGGTGCCCTAGCCCGAGGTGACGGTGCCATTTACTTGCGTTTTCCACACA

upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g08270.1 (Oryza sativa), 3'ss of exon 6
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA
                              || ||||       |    |   || ||| | | | |  |      || | ||    ||   |  ||| ||  || ||||     |   |||||||| ||| |  |||| || ||||| |||||||||||||||||||||||||| ||| |  |   ||| ||||| || || |||| ||| || || ||||
-----------------------------gttggtccccaaaagttgcatacctaatttgtttctgatat------gaataatcacacaagtaaatct-gattat-attatgc--ttggcagAAACTTGGTATTCAAGCTCCTCCAGTTAGAATTGATAGCCAAGCAAAATATGGTGCTGTAGCCCAAGGTGATGGCGCCATTTATTGGCGATTTCCACACA

upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G152757_T04 (Zea mays), 3'ss of exon 6
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA
                                              |   ||  |   | |  |||   |  |  | ||  |    |   ||||   |   |   | ||        | |||||||| |||||| |||| || ||||| ||||| || ||||||||||||||||| ||| || |  |||| ||||| || || || ||||| || || ||||
---------------------------------------------gtagcttccaaactattctttgcttactcgatatccacag-gagtacataagtaatctggttttttaatgctatcagAAACTTGGTGTCCAAGCTCCTCCAGTTAGAATCGACAGCCAAGCAAAATATGGTGCTCTGGCCCGAGGTGATGGCGCCATTTACTTGCGCTTTCCACACA

upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G63980.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattact-tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA
                       |||  |  || |    || ||| |  ||          ||  |||||   | |    | |||  ||  |||||  | |   |   |  | | ||  ||||||||||||||||||||| ||||||||| | ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| || || || ||||| |
----------------------gtaaattgcttctttccttccatgtgattccag------ctaatagctaactaa----ttttcctcatccatttgatcatgttctatgttgtaatatacagAAACTCGGTGTCAAAGCTCCACCAGTCCGTATTGATAGCCAAGCAAAGTATGGAGCTTTATCAAGAGGAGATGGAGCTATATACTTACGGTTTCCTCATA

upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 6
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA
                                                 |  |   || |  ||  ||   | |||   || ||||       ||   || | |  |||| ||  |||||||||||| || ||||||||||| ||||| |||||||||||||| || || ||||| ||| | || |||||||||||||| || ||| | || |||||||| |
------------------------------------------------gtactgtattgtctttgcagacgtctta---ttgttctctctgtcttatatgccta--attattttctgaacagAAACTTGGAGTCAAAGCACCCCCAGTTAGAATTGATAGCCAGGCGAAGTATGGGGCTCTATCCAGAGGAGATGGGGCCATTTATCTTCGCTTCCCTCATA

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|209712036|gb|BW674181.1|BW674181
EST:     CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA                         AAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
genomic: CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgt ... tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
EST: gi|13311617|gb|BG405268.1|BG405268
EST:     CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTTCATTGCAGAA                         AAACTCGGTGTCAAAGCACCACCA
genomic: CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgt ... tcatgaacagAAACTCGGTGTCAAAGCACCACCA
EST: gi|12497023|gb|BG047358.1|BG047358
EST:     CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA                         AAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
genomic: CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgt ... tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
EST: gi|207701824|gb|GD682495.1|GD682495
EST:     CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA                         AAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
genomic: CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgt ... tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
EST: gi|51344888|gb|CO985621.1|CO985621
EST:     CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA                         AAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
genomic: CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgt ... tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
EST: gi|6725411|gb|AW309810.1|AW309810
EST:     CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAA                         AAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT
genomic: CTTTTGAAGCAGCACACTCCTCACATGACTTATCTAGCTCCATTGCAGAAgtaatactgt ... tcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA
                            tcttgac  putative branch site (score: 3)
                                        ttacttc  putative PPT
     tttagatttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatactgttagaactagaagttaacatatttgtcctttttcatattttttttagtttttcttttagctcttttagatttattctgcagacatttcttgaccattattacttcatgaacagAAACTCGGTGTCAAAGCACCACCAGTCAGAATTGATAGCCAAGCAAAATATGGAGCTTTGTCAAGAGGAGATGGGGCTATATATTTGCGTTTCCCTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG