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'   
10  
 5'  3'   
11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcactactatgtttattgtacgttagcatgtaatattcatcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA

Basic information

species Glycine max
transcript GLYMA05G30130.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g39570.5 (Oryza sativa), 3'ss of exon 7
cttcactactatgtttattgtacgtt-agcatgtaatattca--tcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattcctt-cagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA
|| | | | ||| || | ||||| || | ||| | || | | || | || || | ||| | ||| | |||||| |||||||||| || ||||||| ||||| || ||| ||||| ||||| |||||||||||||| || |||||| | |||||||| || |
----gtctctgtagctctaagctgttcagtgttaaatatacatgttaatgtatacaaaattaaggatgcaggtcctaagctaaatatgattttatttggtgcagTCAAGTGGACTTCGATCACATACTCTATCCATCCTTGTCAATGATTGCCCTGGTGTTCTCAACATTGTTACAGGGGTCTTTGCTCGCAGAGGCTACAATA

upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ21245 (Selaginella moellendorffii), 3'ss of exon 6
cttcactactatgtttattgtacgttagcatgtaatattcatcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattcctt----cagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA
| || | || | || || | | | | || || ||| | | ||| | || ||||||||||| ||| | ||||||||||||||||||||| | || ||| || || || ||||| ||| | || |||||||
---------------------------------------------------gtattgtgtttttctcttggttttcatttaaaccgctttctttctcattgcagCCGAATGGTTATATGTCGCACACGTTATCAATGGTGGTGAACGATGCTCCTGGAGTTTTGAATCGTGTGACTGGTGTGTTTGCCAGACGGGGTTATAACA

upper sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ19301 (Selaginella moellendorffii), 3'ss of exon 6
cttcactactatgtttattgtacgttagcatgtaatattcatcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattcctt----cagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA
| || | | || | || || | | | | || || ||| | | ||| | || ||||||||||| ||| | ||||||||||||||||||||| | || ||| || || || ||||| ||| | || |||||||
---------------------------------------------------gtattatgtttttctcttggttttcatttaaaccgctttctttctcattgcagCCGAATGGTTATATGTCGCACACGTTATCAATGGTGGTGAACGATGCTCCTGGAGTTTTGAATCGTGTGACTGGTGTGTTTGCCAGACGGGGTTATAACA

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|13477909|gb|BG507593.1|BG507593
EST:     CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGAT                         ACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
genomic: CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGATgtaagtggtt ... attccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
EST: gi|27446310|gb|CA953433.1|CA953433
EST:     CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGAT                         ACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
genomic: CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGATgtaagtggtt ... attccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
EST: gi|298188621|gb|HO035314.1|HO035314
EST:     CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAGGAT                         ACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
genomic: CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGATgtaagtggtt ... attccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
EST: gi|27427411|gb|CA938931.1|CA938931
EST:     CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGAT                         ACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
genomic: CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGATgtaagtggtt ... attccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
EST: gi|6725650|gb|AW310049.1|AW310049
EST:     CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGAT                         ACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT
genomic: CAGTCAATCAAGTTCTTGACGCTCACTGGGGTGTCCTCAATGATGAAGATgtaagtggtt ... attccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgaatgacatgcttgtgactgtcttactgttggtggaataattccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA
                         gtcttac  putative branch site (score: 3)
 ttccttc  putative PPT
 aataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcactactatgtttattgtacgttagcatgtaatattcatcaattttatgaatgacatgcttgtgactgtcttactgttggtggaataattccttcagACCAGTGGAATTCGATCACACACGTTATCCATGCTTGTGAACGATGCTCCTGGAGTTCTAAACATTGTTACAGGAGTTTTTGCTAGAAGAGGCTATAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
cttcact
- - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgga