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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatgataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC

Basic information

species Glycine max
transcript GLYMA19G24250.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 9
-----------------------------aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatca-tatgataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
                               |||   | |||   | || || |   | | | |  |     |  |||  |   |   |   | |  ||  |  | |     | |   ||  ||   ||||||||  | || |||  |||||| |   ||||||||||||| |||||||||||||| || || || |||||||| ||||| || ||  | ||||||||||
gtactttacctttctctattctctacatgtcaatactatattgcagcttgccaatactataatactaagagtattatgttttagtccgtttctttagtactaaataaaaccagttccctgttaatgccagGTTCTGCAGTCCGTGAACCCTATAAAGCATGATGAGGTTGTCCTTGGACAATACGAGGGGTACAAGGATGACCCTACAGTGCCAGATGACTCAAACACCC

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 10
---aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatgataacacttta-tggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
   ||||| ||        | |||| | | ||    |||   |  |    ||| | |  |   ||  |  |  | | ||| || ||  | || |  || | ||||| ||| |||| ||| | || || || ||||| ||||| |||||||||||||||||||| ||||  |||||    || || ||  || | |||||||| |
ttaaaaatctccttagcgagtttacatggattggttgata--tttccatttgcattttca-gccaattagtctctcgttactgattatttta-gtgaacttcagGTGCTTCAATCTGTGGTTCCGATAAGCGATGACGAGGTAGTTCTTGGACAATACGAAGGATATAGGGATGATGATACTGTTCCAAACGACTCAAACACTC

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 11
------aaaattt-------cacatttatggttacctagtttttgaga--tgagtcaca---------gcatgcctctatatatcatat-gataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
      | | |||       ||||| | | ||| |  | ||||  |||    ||| | |         ||||        |  | ||||  ||||||  | |  | |    ||    || | ||||||||| |||| ||| | || || | |||||| ||||| |||||||||||||| ||||| |||| |||||| ||||| || ||  |  | |||||||| |
gtgattacagttttcttgatcacatctttagtttcaaacttttgtagaatcaagtgatatcttcatttgcattttcagccaattaatattaataacaactgactgatttcttaaatgaacttcagGTTCTTCAATCTGTGATTCCCATAAAAGATGAAGAGGTGGTTCTTGGACAATATGAAGGATATAGAGATGATCCAACTGTTCCAAATGACTCAAACACTC

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 10
aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatg--ataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
|   | |   |  || |||   |||  ||||| || |  ||        ||  || || || | |    || ||||| ||  |||  || |||||  | ||||||||| |||||||||| |||||||  |||||||||||||||||||||||||||||||| || | ||||||||||||||| ||||||   ||||| ||||
actctcttttagataaggtcctctatattttgtgaggtttctgtattgtcccatacatgtcgtttcctgtaccacttgataattgtgatgtgaaa--ttcagGTTCTTCAATCAGTGCTTCCTATTACTGATGATGAGGTTGTTCTTGGACAATACGAAGGTTACACAGATGACCCAACAGTTCCTGACCTTTCAAATACCC

upper sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ21593 (Selaginella moellendorffii), 3'ss of exon 9
aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatgataacactttatggttgctatatgaaaaat-gcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
                                                         ||   ||| | |   |   |  |     || | |||  |  ||||||||  || |  | |  || ||   |||    ||||||||| ||||||||||||||||||||| ||| || || || ||  | ||  |||||   || |
--------------------------------------------------------gtactgtatcacatttccgcacagaataaatctcaaagctcacagGTTCTGCAAGCCATTCAACCAATACAAGACAGCGAGGTTGTTATTGGACAATACGAAGGCTATAGAGACGATCCCACGGTTTCCGATGAGTCATTGACAC

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|151404199|gb|EV274009.1|EV274009
EST:     TTTCTCTCAGGCCTGAGCACATTCGGGAGGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA
genomic: TTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... aaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA
EST: gi|254338293|gb|GR849818.1|GR849818
EST:     AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAG                         GTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA
genomic: AAAAACCAGTTTCTCTCAGGCCTGAGCACATTCGGGATGAGAAAGTGAAGgtgtgcctct ... aaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcctctatatatcatatgataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC
                   tgataac  putative branch site (score: 2)
        tatatatcatatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatttcacatttatggttacctagtttttgagatgagtcacagcatgcctctatatatcatatgataacactttatggttgctatatgaaaaatgcagGTTCTTGAATCAGTGCTCCCTATTAGAGATGATGAGGTTGTTCTTGGACAATACGAAGGCTATAAAGATGACCCAACAGTACCTGACAAGTCAAACACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG