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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtccgcctccgtcccctggactgcgtgtgtgtgcttgagctgaggctgagtctgagtctggccccgccggcgccgcgggctggctgttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA

Basic information

species Zea mays
transcript GRMZM2G458549_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 1
gtccgtccgcctccgtcccctggactgcgtgtgtgtgcttgagctgaggc-tgagtctgagtctggccccgccggcgccgcgggc-tggctgttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA
    ||  |             |  | |   | |  | ||  |  || || |  |  |   |||| |   |  ||    ||| |   |  |||   ||||||| |||| |||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||||||| | |||||  |
----gtaggttgatagatggatgggtaccactctaggtttcggtggatgcgtttgatttgatctgacaaggatgg-attgcgtgtgcgtgtgtgtgtgcagGGCGGGTGAATCTGATAGGGGAGCACATCGACTACGAGGGGTACTCGGTGTTGCCCATGGCCATCCGGCAGGACATGATCGTCGCCATCAGGAGGGCAGA

upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------gtccgtccgcctccgtcccctggactgcgtgtgtgtgcttgagctgaggctgagtctgagtctggccccgccggcgccgcgggctggctgttgc-tgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA
                                                                                                      |  |   |    | ||   ||  || | ||| ||   ||  | ||    ||| | |||   | |    |  |  |  |   | |   | |||  || ||| || || |||||||| || |||||||| ||||| || || ||||| |||||||||||||| || || ||||| |  ||  | || || || |      |
gtaaataatctcgggtttttgaatttttgcaaaaattggaatttcgttgactttgagatgaattggtttctaattattgtatcgatgtctgcaattttggtatttggatgatgacatcagatgatcttc-tgtttggaatt--gttggatatgattgtgaaaatagat--ggtgaaggtgtttgttatattttgtgtgtagGAAGAGTGAATCTGATAGGAGAGCACATTGACTATGAAGGATACTCAGTGTTGCCGATGGCTATTCGTCAGGATACAATTATAGCGATTCGGAAATGTGA

upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------------------------------------------------gtccgtccgcctccgtcccctggactgcg-tgtgtgtgcttgagctga--ggctgagtctgagtctggccccgccggcgccgcgggctggctgttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA
                                                                                |  |   |  |  ||     ||| || | || || ||  |||  |||  |   |||| |  |   |     |  ||          |   | | | |||||||||||| ||| |||| || |||||||| || || || ||||| ||||||||||||||||| || || ||||||| |||||| || || || | |    |
gtcggtaacacgcgtgttcatagtttttctgttggtcgtgtattgtatgacgaggaaaaggaggagatttttggagtttttgtgagtgggtgtgtggtggggattgtggtgggtttggatga-ttgattgatggagtatcgggaggtttttgatggttttattttttatttttgggtgcagGGAGGGTGAATTTGATAGGAGAGCACATTGATTATGAAGGCTATTCGGTGTTGCCGATGGCAATACGGCAGGACACGATCGTGGCGATTCGGAAGCATGA

upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ17214 (Selaginella moellendorffii), 3'ss of exon 1
gtccgtccgcctccgtcccctggactgcgtgtgtgtgcttgagctgaggctgagtctgagtctggccccgccggcgccgcgggctggctgttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA
                                || | |||||  |   |||   | || |   |        ||||    | |    | |    ||||||  | || ||||| ||||| ||||||||||| ||||| |||||||||||| |||| ||||| || ||||||||||  || ||||| ||  | ||  ||  
--------------------------------gttttcttgatatttcgctcgatttgtg---gattggattggcgattggcggctcccgggaatgcagGTCGAGTGAATCTTATCGGCGAGCACATCGATTACGAAGGCTACTCGGTGCTGCCAATGGCAATTCGCCAGGACACAATTGTCGCGATTGGGAGATCCTC

upper sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30960 (Selaginella moellendorffii), 3'ss of exon 1
gtccgtccgcctccgtcccctggactgcgtgtgtgtgcttgagctgaggctgagtctgagtctggccccgccggcgccgcgggctggctgttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA
                                || | |||||  |   |||   | || |   |        ||||    | |    | |    ||||||  | || ||||| ||||| ||||||||||| ||||| |||||||||||| |||| ||||| ||||||||||||| ||| ||||| ||  | ||  ||  
--------------------------------gttttcttgatattttgctcgatttgtg---gattggattggcgattggcggctcccgggaatgcagGTCGAGTGAATCTTATCGGCGAGCACATCGATTACGAAGGCTACTCGGTGCTGCCAATGGCAATCCGCCAGGACACGATTGTCGCGATTGGGAGATCCTC

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|148997911|gb|EE035899.2|EE035899
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|76290432|gb|DV030000.1|DV030000
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148960156|gb|EE153406.2|EE153406
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|71773516|gb|DR971416.1|DR971416
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|76283981|gb|DV023549.1|DV023549
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|89764289|gb|DY691150.1|DY691150
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|93014044|gb|EB639564.1|EB639564
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148955644|gb|EC901316.2|EC901316
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|149070820|gb|EE159229.2|EE159229
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|74231838|gb|DT639752.1|DT639752
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148972046|gb|EE022887.2|EE022887
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148982924|gb|EE028793.2|EE028793
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGGGAGGGTCTCTCTGATCGAGGAGCACATCGACTACGAGGGCTACTCGGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGG--AGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGT
EST: gi|149071533|gb|EE159924.2|EE159924
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|76912626|gb|DV164825.1|DV164825
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148965140|gb|EE015956.2|EE015956
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|78085244|gb|DV513637.1|DV513637
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|93282954|gb|EB675218.1|EB675218
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148991238|gb|EE032704.2|EE032704
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148951727|gb|EC897480.2|EC897480
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|71318360|gb|DR795942.1|DR795942
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148973013|gb|EE024065.2|EE024065
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148942675|gb|EC887696.2|EC887696
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
EST: gi|148967123|gb|EE018297.2|EE018297
EST:     CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAG                         GGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT
genomic: CTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGT

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), 47 (downstream exon)
Score: 61

GGCGCGCAGCTCGACGAGTCGCGCCTCCGCTTCGCCCGCCTCGGGGACCGCTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 159

GGCGCGCAGCTCGACGAGTCGCGCCTCCGCTTCGCCCGCCTCGGGGACCGCTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 212

GGCGCGCAGCTCGACGAGTCGCGCCTCCGCTTCGCCCGCCTCGGGGACCGCTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GGCGCGCAGCTCGACGAGTCGCGCCTCCGCTTCGCCCGCCTCGGGGACCGCTTCCACGCCGTCTACGGCGCCCGCCCCGCGCTCTTCGCCCGCTCCCCAGgtccgtccgc ... gttgctgcagGGAGGGTCAATCTGATCGGGGAGCACATCGACTACGAGGGCTACTCGGTGTTGCCGATGGCCATCCGCCAGGACATGATCGTCGCCATCCGAAGGGCCAA