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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA

Basic information

species Glycine max
transcript GLYMA14G11220.2
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------------tttgtagtgtttcatttattataatggtattttatt-atcattctgcctatt--taaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
                                                                                                               |   | | || ||| | ||       || || ||  ||   | ||  | ||   | | | |  ||   |  || |||        | | |||  | |  ||   | |      ||||||||||| || || ||||| ||||| |||||| | | |||||| |||||||| ||||||||||||||                  
gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGC-ACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------

upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 24
----------------------------------------------------------------tttg--tagtgtttcatttatta-taatggtattttattatcattctgcctat---ttaaacttaagttgacaagttactgactgcataa-gctatgttattg-----acagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
                                                                || |  || | | |  |  |  | | || ||||||  | |    | ||  | |   | | |  |  ||| |      |   ||   | |  ||| | |  |||     ||||| |        || || ||||| || || |||||||||||  |  | || | ||| || || ||||| |||| ||||||||||||||| |||||||||||
gtaatgcatctgcaaggagttttgctcaacaaatcaactcatttctctcctgccaagttcaatattaggatactatcttgtccagcaattattgtatttagtcaattgtttgtttttacctgataactgggttaatggtagagcaacactaaagcgctgtatatttgctgtcacagTGAGCAATGTTCCCCCCAAGCTGGTTATCCTTCATATGAACCTTTCCCTTCTTGTATACGAGGATATAATGACGATGACTGAAAACCTGAGTGAGAAGTA

upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
----tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
         ||| ||| ||||  || | |  ||  |  |    | |         || |      |||| |   |  ||     ||     ||  | ||  |||| |        || || ||||| ||||| ||||||||||| ||||| || ||||| | ||| ||||| |||||||||||||| ||| | |||||||| ||
attcaactcagtattttattttgta-agttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatat---tcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA

upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 24
tttgtagtgtttcatttat-tataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgc-ataagctatgttatt--gacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
  || |||     ||| |  |||  ||  |  ||||     || | |   | | || | ||    |  | | |   ||||  | |    |  ||  |    ||   ||   |   | ||| ||||| ||||| || || ||||| ||||| ||  |||| ||||| ||||| |||||||||||||||||| | || || ||   
cctg-agttcagaattcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactgtgacagataaccttgcttcagCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGAAAACTTGAGCGAAAA---

upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
tttgtagtgtttcatttattata-atggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
              | || | |  |    | ||||  |   |||| |  |  || | |  | |  |  ||||| |   |  ||   ||  | |     |||| | ||  ||  | || ||||| || || ||||||||||| |||||||| || || || || ||||||||||| ||||| || || ||||||||||||||
-------------gtctactctccaaaccactttacgaatgttcttc--acctacaatgtaatccaatagttaatccttaaatttcct--ggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA

upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
-----tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
     | ||||    || || |||| | |    | | | |||  ||| | ||| || ||||||    |  | |  |||| |||     || |   | |   |||||||  | |||  | || ||||| ||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| |||||| | |||||||||||
ttatatctgtatcccttaatatattttgaaa--aatgtgttactattttcccttttgaaactt---ctctccatctactaactaatgtagtttgctaaacaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTA

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|15287884|gb|BI471775.1|BI471775
EST:     CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAA                         TTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
genomic: CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAAgtacttatct ... ttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
EST: gi|27424345|gb|CA935865.1|CA935865
EST:     CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAA                         TTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
genomic: CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAAgtacttatct ... ttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
                         tactgac  putative branch site (score: 1)
     ttaaacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcataa