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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagtctttggttttgacgtgtttgtgtttccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC

Basic information

species Zea mays
transcript GRMZM5G868757_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 5
tgagtctttggttttgacgtgtttgtgtttccattgttt--catttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
 |   | | |||  ||   | |   ||   ||||   ||  |||   | |     |    | | |||      | |  |||  || ||         |||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||| ||||
-ggagcctgggtgctg-tatttccatgaggccatcaattgccatacaatttaaaagtaaattggaatatgagagaattattaatgattcccccattttgcagGTTCATCTTATAGAGGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTAGAGTACTTGGAATTCCACAGGTGAAGGCGTTGC

upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g32800.2 (Oryza sativa), 3'ss of exon 5
-------tgagtctttggttttgacgtgtttgtgtt--tccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
         ||||||   || |||   |   |   |  || | | ||  | ||   |   | ||   | ||    ||  ||  |      ||| || | || | |||||||||||||||| || || ||||||||||| |||||||| ||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||| ||||
atgctagaaagtcttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgc---tagtgtatcagctgcca------tgcattttctccactgcagGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTAGAGTACTTGGAATTCCACAGGTGAAGGCCTTGC

upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------tgagtctttggttttgacgtgtttgtgtt--tccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
                                          ||||||   || |||   |   |   |  || | | ||  | ||   |   | ||   | ||    ||  ||  |      ||| || | || | |||||||||||||||| || || ||||||||||| |||||||| ||||||||||| ||||||||||||||||                                 
ctagattcattagcatctatatgaatgtgggcaatgctagaaagtcttacattgtgaaacggagggagtagtcaaatattgaaattattttagtcgc---tagTGTATCAGCTGCCA------TGCATTTTCTCCACTGCAGGTTCATCTTATAGAAGGGATAATTGATGAGGTGGACAGCACAGTTCACGTGTCATGGGTCCAGCCTA---------------------------------

upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G01460.1 (Glycine max), 3'ss of exon 5
---------tgagtctttggttttgacgtgtttgtgtttccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
         ||| | | ||  ||||| |   ||| ||||  |||||     || ||  | ||        |||    |||||||      ||  || ||| || ||||||||||||| |||||||| ||||||||| |||| ||  | ||||| ||||| || ||||| ||||| ||||| || || |||| |||| | ||  | || |
tatcttttttgaatttctgcatttga-gaacttgagtttt-attgtcattcttaacaacattttaaaatttaaa--gcttgtaag-----tgaattttttgaattgcagGTTCATCTAATTGAGGGTATAATTGATCAAGTTGAGGGCACAGTCCACGTTTCTTGGGTGCAGCCAAGAGTTCTGGGTATTCAACAGATCAAATCCTTAC

upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 6
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 5
tgagtctttggttttgacgtgtttgtgtttccattgtttcatttgactgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaa----tgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
   || |    || | | ||  |  | |     || |   |  || |         | | ||| |  ||     | |  || | |     |   |    |||||||||||||||||||||| || |||||| |||| ||  | |||||||| || || ||||| ||||| |||||  | || ||||||||| | ||  | ||||
---gtatccacttgttaagtagtcatttacttgttttgggaaatg-caattcaagcttttgtattaaaccctgtagacattggttaaaacttggactgctgcagGTTCATCTTATTGAGGGCATCATTGATCAAGTTGAAGGGACAGTTCATGTGTCGTGGGTGCAGCCAAGAGTTTTGGGTATTCCACAGATCAAATCGTTGC

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|194716906|gb|FK934065.1|FK934065
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTAC
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTAC
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     CTAAGCTTTCAATCAGTGACGTGAAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|4609963|gb|AI600802.1|AI600802
EST:     AAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: AAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|4804325|gb|AI666191.1|AI666191
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|6020410|gb|AW065338.1|AW065338
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|60336794|gb|DN203767.1|DN203767
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
EST: gi|211013700|gb|FL252294.1|FL252294
EST:     CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG                         GTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA
genomic: CTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 254

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 304

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

TCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCGgtaacttgat ... tcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgccttgcgtctggtaatccacttgtaacatttttgctttgtttcaaatgcagGTTCATCTTATTGAGGGAATAATTGATGAAGTGGACAGTACAGTTCACGTATCATGGGTCCAGCCTAGAGTGCTTGGAATTCCACAGGTTAAGGCTTTGC
                        ttgtaac  putative branch site (score: 212)
                                tttttgctttgtttc  CT-rich tract
                           taacattttt  TA-rich tract