Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacatctgctgagaaatgacatcttggtttttattgtgtctttcatattttaatcatgtggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT

Basic information

species Glycine max
transcript GLYMA04G04120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G04120.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G131638_T01 (Zea mays), 3'ss of exon 3
-ccacatctgctgagaaatgacatcttggtttttattgtgtctttcatattttaatcatgtggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
 | | |  |      || |    |||  | ||         |  | |      |  |||| | |    |     | | || |  |     ||  |||  ||||||||||||| ||||| |||||||||||| |||| ||||| |||||||||| ||| ||| | |||||||||   || || ||| |  |    || ||||
gctagaaatatcccaaactctattctctgattaacaaaaacccattacccaccag-catgagcattcgttgacatttgatcctcatccgatgattgcgcagGTGACAGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCCACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCTTGCAGGTGAAGAACAGCCACCACGAGT

upper sequence: GLYMA04G04120.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G363474_T02 (Zea mays), 3'ss of exon 2
--ccacatctgctgagaaatgacatcttggtttttattgtgtctttcatattttaatcatgtggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
  |    |   |  | |||  ||   ||       |    |  |         |   ||| ||     || |      |  |||||    |  | |||  ||||||| ||||| ||||| |||||||||||| |||| || || |||||||||| ||| ||| | ||||||||||  || || ||| |  |    || ||||
ctctgatttaacaaaaaaaaaaccagttacccaccacccagcatgagcggacatgtgcatttgttggcatttgagctctcgtccaatgatt--gttgcgcagGTGACGGAGAACGGGAAGCAGGAGCGGCATCTAGTGGCGACGGTGGGGAAGTACAGCGTGGTGTGGAACTTCCTGCAGGTGAAGAACAGCCACCACGAGT

upper sequence: GLYMA04G04120.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G33400.1 (Arabidopsis thaliana), 3'ss of exon 1
ccacatctgctgagaaatgacatcttggtttttattgtgtctttc--atattttaatcatg----tggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
      || |||   ||| |    |   ||   ||    | || |  ||| || | || ||    |     | ||| |||  |  |  ||  | | | ||   ||||| || ||| |||||||||||||||| ||| | ||||| ||||| || ||||||||||||||||||||||| || || || ||| |||| |||||||| |
-----actactgttgaatcattcatcaattgaaataactttttactaatagttgattcctgactctttttgtctatcttttcttgttgaaaatgtcg-atatatagGTCACGGAGGATGGGAAACAGGAGCGTCATGTGGTAGCTACTGTTGGCAAGTTCAGTGTGATATGGAACTTTCAGCAGGTGAAGAATGGATCTCATGAAT

upper sequence: GLYMA04G04120.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10540.t01 (Vitis vinifera), 3'ss of exon 1
-ccacatctgctgagaaatgacatcttggtttttattgtgtctttcatattttaatcatgtggaaatatatttttattattccaacttcttgga--tgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
   |    | || | | ||| || | || ||| | || | || || ||  ||   || |  |    ||  | | |  |  |||||| | ||| |  | | ||||| |||||||||||||| |||||||| ||  | || ||||| || || ||||| |||||||||||||| || ||||| || ||| |||| || |||||||
tgtattctttcttatacatg-cagcatg-tttctcttatatcctt-atgattggttctttggcttttaactgtcttgtggtccaacattttgaaattccatagGTCACAGAGAATGGGAAGCAGGAGCGCCACCTGGTTGCCACAGTAGGAAAGTTTAGTGTGATATGGAATTTTCAACAGGTGAAGAATGGCTCCCATGAGT

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|16996822|gb|BM086194.1|BM086194
EST:     CACATTTGGCTGGAGCAAATAACAAGTTCCGCAATGCTCAGTTTTCGTGG                         GTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAG
genomic: CACATTTGGCTGGAGCAAATAACAAGTTCCGCAATGCTCAGTTTTCGTGGgtaagtataa ... ggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAG
EST: gi|18039585|gb|BM307879.1|BM307879
EST:     CACATTTGGCTGGAGCAAATAACAAGTTCCGCAATGCTCAGTTTTCGTGG                         GTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAG
genomic: CACATTTGGCTGGAGCAAATAACAAGTTCCGCAATGCTCAGTTTTCGTGGgtaagtataa ... ggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttaatcatgtggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT
   ttttaat  putative branch site (score: 3)
                                       cttcttg  putative PPT
     ttaatcatgtggaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacatctgctgagaaatgacatcttggtttttattgtgtctttcatattttaatcatgtggaaatatatttttattattccaacttcttggatgcttagGTGACAGAGAATGGGAAACAGGAGCGGCATATAGTAGCCACTGTGGGGAAGTTCAGTGTGATATGGAACTTCCAACAAGTCAAGGATGGTTCTCATGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
ccacatc
- - - -tgctgag
- - - - - - - - -tgacatc
- - - - - - - - - - - - - - - - - - gtgtctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccaact