Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   
7  
 5'  3'   
8  
 5'  3'   
9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA

Basic information

species Glycine max
transcript GLYMA18G00720.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 13
gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
| | |||| |||| | || ||| | |||| | | | | | | | ||| | ||| |||| |||| ||| | | | | | ||| ||| ||||||||||||||||| ||||| ||||| ||||| || || | ||||| || ||||| |||||||||||| ||||||| ||||||||||| || |||
---------------------gtgaggat-atttgctgaagacacttcctgacagataaccataagtagctctagctctga--taattttatgtg----ttgttttct-aatgtttgtattctggcttgctttga--cagATCGGTTTACAAAACTGTCCCAAACTGTGAGCCTTGCCGGCCTCTCCAAAGGTCACCTATCGAAGGTTTCTATCTAGCTGGTGATTACACAAAGCAGAAA

upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 13
gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
|| | ||| || | || | | | || | | ||||| | | || | | | ||| | ||| || || ||||| || | ||||| |||||||| ||||| || | |||||||| ||||| ||||| ||||| ||||||||||||||||||||||| ||
---------------------------------------------gttagtgaagttgtaccatttatttagcttcaaatgagggaccaggctttacattgataaattcaacatctttctctattgttgcatgat--cagATCTGTGTACAAGACCATCCCAAACTGTGAACCATGTCGTCCTCTACAAAGATCACCTATTGAAGGATTCTACTTAGCTGGAGATTACACAAAACAGAAG

upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 13
gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatt-tgtgttctga-atcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
| || |||| | | | | || | || || | ||| || || | || | || | | | | | | | || | || ||||| || |||||||||||||| ||||||||||||||||| || ||| | ||||||||||||||||| || || ||||||||||| || |||||||||||||||
----------------------------------------gttttttttttccacgtcaagttattgccttttgattttcgtttatttagtactattatagcatattgtaataattttaagctattggattca--acttcagATCTGTTTACAAAACTGTCCCAAATTGTGAACCTTGCCGTCCCTTACAAAGATCTCCTATAGAGGGCTTTTATTTAGCTGGGGACTACACAAAACAAAAA

upper sequence: GLYMA18G00720.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S369_27V6.1 (Physcomitrella patens), 3'ss of exon 9
--gtttgattgaatacccacagagggtggattatttctttta-gcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatt-tgtgttc-----tgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
| ||| | | | || | || | || ||| ||| | || |||| ||| |||| | || | || | ||| || || ||| | | ||| | || | || ||| |||||||||||||||||| || || ||| ||||||| |||||| | || |||||||||| ||||| | ||||| | || || || | ||| || || ||
gtactaagaactttacaccctactgtgggctcatctgcactatgctaaatttcttttaat---tttgccgtgtgtttgatttttcgcaagcaccagtagttttatgaattcacgagtaagcccttttctgaccg-ctgcatc-tttcagGTCGGTTTACAAGACGGTGCCAGATTGTGAGCCTTGTAGGCCACTTCAAAGATCACCTATTCCAAAGTTCTACATGGCGGGTGACTTCACTAAGCAGAAG

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|31460437|gb|CD402405.1|CD402405
EST:     AGCAAAGCTAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCGGTTTACAAAACTGTTCCAAATTGTGAACCTGGTCGACCCATTCAAAG
genomic: AGCAAAGCTAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAG
EST: gi|192309609|gb|FK002889.1|FK002889
EST:     GACCAAAGCAAAGCTAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAG
genomic: GACCAAAGCAAAGCTAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAG
EST: gi|192309608|gb|FK002888.1|FK002888
EST:     GACCAAAGCAAAGCTAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAG
genomic: GACCAAAGCAAAGCTAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA
                                   aactgac  putative branch site (score: 2)
 ttgtttc  putative PPT
 attgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgattgaatacccacagagggtggattatttcttttagcttcttttataaagatggatttggaatgtctttgttgttacttaactaatagtgacatttgtgttctgaatcctaatggaactgactacattgtttcagGTCGGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGACCCATTCAAAGATCTCCTATAGAAGGTTTCTATTTAGCTGGAGATTACACAAAACAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT