ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttttgaactatcactttagccttttccattacatttattatcttcaaaatatccatgtatgaaactttgatggtactctggcatttgagaaaatattttttccttaatataaagaaac

Basic information

species	Zea mays
transcript	GRMZM5G845682_T02
intron #	2
splice site	5'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g44560.1 (Oryza sativa), 5'ss of exon 15

--------------------------------------GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttttgaactatcactttagccttttccattacatttattatcttcaaaatatccatgtatgaaactttgatggtactctggcatttgagaaaatattttttccttaatataaagaaac
                                      |||| |||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||||| || ||| | || ||||||||||||||||||| | |||||||||||| |    | |  ||  | |||   |||| |||| |  |    |   | |   |                                                              
TTACAGGGCTTTAAATGATTTATTTGATATCTCACTAAGTAGGAGAAATGCTTTCTCTTATGAGGTGGGAGTTCAGATGGTTGAGATATACAATGAACAAgtgcgggatcttctgtcaaatgatattgcacagaaacgatatcctttttcatac-ttaaattgtcatttctaattatatttctggtacctatgtttttagt--------------------------------------------------------------

upper sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G01800.1 (Glycine max), 5'ss of exon 15

-------------GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttttgaactatcactttagccttttccattacatttattatcttcaaaatatccatgtatgaaactttgatggtactctggcatt-tgagaaaatattttttccttaatataaagaaac
             |||| ||||   |  |    ||||| || || ||||| |||||||| || || || ||||||||||||||||| ||||||||  ||  | | || |  ||||||||||||          ||||||  | |      | ||  |  ||  |   |       | ||  |  ||| | |  || |      || || ||                            
CATATCTCCCAGAGTAGGAGAAGCTCTATTGTTTATGAAGTTGGAGTACAAATGGTTGAAATTTATAACGAACAAGTTCGTGATTTACTATCAAACAATGgtcctcaaaagagatatcctttt----------ctttagtatatattcccagatccacaatagtgggagc-cttgtatactaggcttcgcttttaattataagttatgtga----------------------------

upper sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 5'ss of exon 14

-------------------GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttttgaactatcactttagccttttccattacatttattatcttcaaaatatccatgtatgaaactttgatg-gtactctggc-----atttgag-----aaaatatt-ttttccttaatataaagaaac---
                      | | ||    | |  | ||||| || || || |||||||| |||||||||||||||||||| || ||||| || ||   ||| | | | || |  | |||||||||||        ||||     |||| | ||     | | |  || |     ||||  ||||||  || | |  || |||   |      |||| |     |  || || |||||||| |  |  | | ||   
CTCTTCAGAATCTCTCAATCCCGTAAAAGCAACATAGCGTATGAAGTTGGGGTGCAGATGGTGGAGATATACAATGAACAAGTGCGCGATTTACTCTCTGgtgacagttctcaaaagaaatatccttttttgtgctctacttacttttttttcttttgccctttcaaatttagttcctcca--tatgaattttggctctgttctccaactttctgtttgtgtttccattatgttgttttccttgactttcacacactag

upper sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 5'ss of exon 13

-------------GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttttgaact--atca--ctttagccttttccattacatttattatcttcaaaatatccatgtatgaaactttgatggtactctggcatttgaga----aaatattttttccttaatataaagaaac--
             |||||  |||  |  |    ||||| || ||||| || ||||||||||| |||||||| |||||||||||  | || ||  | |||  | |  | |  |||||||||| |  ||    || |    || | | |||  |||    | ||| | || |   ||  ||  ||| ||| ||   |      |   || ||| ||     |||| || ||    || ||       |  
CACTTAACTCAAAGTAGACAAAACTCAGTGATGTATGAAGTTGGTGTTCAAATGGTTGAGATTTACAATGAGCAAGTTCGTGACCTACTTTCTCAGGATGgtcctaataagagatatccttctctaatctaattaagtatttgacatttttattgatatcattttttttatgtta--caaatattaaatttccttaacttgcatacacttgggatttggaatacttctttaccaa-atggcctcgcag

upper sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 5'ss of exon 14

-------------GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttttgaactatcactttagccttttccattacatttattatcttcaaaatatccatgtatgaa-actttgatggtactctggcatttgagaaaatattttttccttaatataaagaaac
             | || ||||   | ||    |||||  | || || || |||||||| ||||||||||||||||| |||||||| ||||||| ||||| | | || | || |||||||| |  |   ||   || |  ||||  ||| |   |     |    |  |||||| | | |    | ||| ||  |    |  |  |                                 
GAGATCACTCAAAGCAGGAGAAGCTCATTTATGTATGAAATTGGAGTTCAAATGGTTGAAATATACAATGAACAAGTGCGTGATTTACTATCAAGTGATAgttctcaaaaaaaatatccttctctattcatt--ttcattctttggcataaagat----gtaaaaaggatatccttctctattcattttcatcttctgttttcgct---------------------------------

upper sequence: GRMZM5G845682_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 5'ss of exon 16

GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatccttt-------ttgaactatcactttagccttttccattacattt-attatcttcaaaatatccatgtatgaaactttgatgg-tactctggcatttgagaaaatattttttccttaatataaagaaac
                          || ||||| || |||||||||||||| ||||||||||| || |||||||| || | ||||  | | |||| ||||||||||||       || ||   |   || |   || |   | |  ||| | || |       | |  |  | |    |||   ||| |   ||   | | ||   |  || | | | ||| |          
--------------------------GTCGGTGTCCAAATGGTTGAGATATATAATGAACAAGTGCGAGATTTGCTCTCGAGTGATGGTTCTCAGAAAAGATATCCTTTCCTTCAATTCAATACTTgtttcaaatttatttgtgaggtttcagtaacagttgggtttttaactttattgcttgactggatgtacttctaatggatggatgatatatcctttattgc--------

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|211520867|gb|FL034524.1|FL034524

EST:     TACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAG                         GCTTGGGATTTGGAGCACTTCTCAACCCAATGGGCTTGTTGTTCCAGATGC
genomic: TACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttt ... ataaagaaacGCTTGGGATTTGGAGCACTTCTCAACCCAATGGGCTTGTTGTTCCAGATGC

EST: gi|61119020|gb|DN559981.1|DN559981

EST:     TACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAG                         ACTTGGGATTTGGAGCACTTCTCAACCCAATGGGCTTGTTGTTCCAGATGC
genomic: TACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttt ... ataaagaaacGCTTGGGATTTGGAGCACTTCTCAACCCAATGGGCTTGTTGTTCCAGATGC

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: 306

GTAGAAGAAATGCCTTCTCATATGAGGTGGGTGTACAGATGGTTGAGATATACAATGAACAAGTTCGTGATTTGCTATCAAATGATATTGCACAGAGAAGatatcctttt ... ataaagaaacGCTTGGGATTTGGAGCACTTCTCAACCCAATGGGCTTGTTGTTCCAGATGCAAGCTTGCACTCAGTTAAGTCGACATCTGATGTATTAGACTTGATGGAA

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 27

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 41