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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

Basic information

species Glycine max
transcript GLYMA16G01230.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 1
cttctctcattctctgtattggtagatac-aatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcatttt-gcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
    |  |||   |     |  |   | | ||  |  ||  | |   |  |   ||    | ||| | ||||||||  ||||| || | || ||||| |||||| || ||||| |  | |||||||||||||||||| |||||| | ||||| |||||||||||
tagtttgcatgtaccaggcttctttttgctaaggcgtttcctattatttgtagatt--tttatttcttctttctttgtttttttacatttttatttttgcagATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 2
cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttccttt--ctttcctttttcacttcttcat-tttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
  | | || || | |   |    |     | | | || |     | |     ||  | || || ||| |    | ||    || ||||| |   | ||||||||| || || ||    |||||||| ||||||||||| |||||| ||||||| |||||||| ||
--tttttctttatttaagtcaa-atgcgaactgcgatatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
cttctctcattctctgtatt---ggtagatacaatacaatttttttccctcttgatttgccctctttttccttt----ctttcctttttcacttcttcat-tttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
         || |||  |||   |  | || | |      || |       | ||| |   |||| ||     |    | ||    || ||||| |   | ||||||||| || || ||    |||||||| ||||||||||| |||||| ||||||| |||||||| ||
--------gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 1
cttctctcattctctgtattggtagat-acaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
 || ||  |   |   |  ||  |  | |  |   ||  ||||| ||| |   | |  | | ||  |  | | |  | |  |    || | | |||||||||| |||||||| |||||||||||||| || ||||||||||||||||||||||||||||||||
-ttatcgtagcttagttgctgagactttaggaagtaaagttttttcctttatttctttctttttcattttctttggcttcctatttttttcctttttgcagATAGAACCAATCCCAAGTGGAAATCTCCCCCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 1
-cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
  ||       | | |   ||           |  |||     |        | ||||  || ||||| |||  || |||| | |||| |     |||||| | || ||  ||||||||||||| || ||||||||||||||||| ||||||||||| || ||
aattgagctgatatttaccttctcgtgcttt-tctaatggggatagaaaagaaattgcaatccttttcattttctttctttcttacttttggcaattgcagTTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 1
cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttc---ttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
 |  |     |   |||    ||||| |        ||||  | | | ||  | |||  || | |     | |||  ||| |   ||    ||  | |||||||| || ||  | ||||||||||| || ||||||||||||||||||| ||||||||| |||||
-tggtaatggtagatgttcgtgtagaaaaggagtggttttggtacttgtt--tctgcaatcatctcttaatgttttgtttatggttttgcatttttgttgcagATGGAGCCTTTACCAAGTGGAAACCTTCCTCCTGGTTTTGATCCAACTACTTGCCGTAGTGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
-cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
  |  | |   |   || |||    |           | | ||    |  |  |||  | |  ||||  ||||||| |||||| || | || ||||||||||| || ||||| |||||||||||||||||||||||||||||| ||||||| |||||||||||
cttgatgtgggtagatg-atttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttttttacatttttattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ13606 (Selaginella moellendorffii), 3'ss of exon 1
cttctctcattctctgtattggtagatacaatac-aatttttttccctcttgatttgccctctttttcctttctttccttt--ttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
   | |               |    |  | ||    |||| |||  ||||  |||    ||||| |  |||  | | |||  ||   |  ||  ||||||||||||| ||||||||||||||||||||||| || || |||||| ||| | |||| ||||||||
---cccgagagaggaaagcgagctcttttagtattggttttgttctttctttttttcttttctttctttttttctgcatttcctttcatcgttttttttgcagATTGAGCCAATTCCAAGTGGAAATCTGCCACCAGGGTTTGATGCAACTTCTTGTCGCAGTGT

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|5606316|gb|AI900414.1|AI900414
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
EST: gi|209725663|gb|BW663152.1|BW663152
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
EST: gi|4313794|gb|AI460913.1|AI460913
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
EST: gi|298165726|gb|HO008697.1|HO008697
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
EST: gi|5058332|gb|AI736808.1|AI736808
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCAAGTGGAAATCTGCCTTCTGGTTTTGATCCAAGTACT
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
EST: gi|5342734|gb|AI795018.1|AI795018
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTAC
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATT-CCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTAC
EST: gi|4282741|gb|AI440569.1|AI440569
EST:     TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAG                         ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT
genomic: TTCTCCAACAACAGTCTCTCTACCACCCTGGTCTCCTTGCTCCTCCTCAGgttggacccc ... cattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
 tcttgat  putative branch site (score: 4)
       tttgccctctttttcc  CT-rich tract
                                           ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctctcattctctgtattggtagatacaatacaatttttttccctcttgatttgccctctttttcctttctttcctttttcacttcttcattttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - -cattctc
- - - - - - - - - - - - - - caataca