ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG

Basic information

species	Zea mays
transcript	GRMZM2G158162_T03
intron #	4
splice site	3'
intron type	U12 (go to U12 genes for details)

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttag--taacttatacatca---aggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttctttta-tcttccttgactatattt---tgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
              || ||| ||   ||  |  | | |||||| |||||| |||   |  |   |  ||   ||  ||    || |   |  ||||  ||  | ||| |  |    ||   || | ||||  ||||||  | | |       | ||| | | |  | ||||  | |||||| |||||||||   | |||||||||||||||| || || ||  |||| |||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatt-tcatattgtgcatacctattt-------ctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                                                                    ||| ||| ||   |  ||| |  ||  |  ||       || | ||  | || |  ||  ||     | | ||||||   |||  |   ||||  || || || || || |||||||| ||||||||  ||||||| ||||||||||| || || || || |||||||| |||||| ||||||| |||
---------------------------------------------------------------------------------------------------gcat-aggttttgcctgttaca-catcgtctatg------ttatata-taaatttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G40280.1 (Glycine max), 3'ss of exon 3

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                                                          || ||||    | |||  ||   |  ||||   |   |  | |   | |||  |  | | || |  ||  ||  |  | | ||||||   |||  |   ||||  || || || || || |||||||||||||||||  ||||||| || |||||||| || || || || |||||||| |||||| |||| || |||
-----------------------------------------------------------------------------------------ttataatataggagtagatttggcctgttatt-caccgtctacattatactt-cgatataaatttgattcatcactagtttcccttgatgttatcatcacagTTTGAAGTCTACTATAGTGCCATTGTTCGAGAAGGTATTGAGTGCCAGCGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGCGCTGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 6

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                                                       |  |   ||   | ||| || |      |||  || || ||  |  |   |||  |   | | |  | |||| |    ||  |||| | | | |||  |   ||||  || |||||  | || ||||| || ||||||||  ||||||| ||||||||||| || || || || |||||||| |||||||| ||||| |||
-----------------------------------------------------------------------------------gtatcctttatattttttatttggttg----tcttg-aacat-atataatagactctgatagtataaagttggtttattcagtagtttcccttaatgtatgat---agTTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g08100.t01 (Vitis vinifera), 3'ss of exon 4

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                     |   |  | | ||||  ||  ||| |  |  | | |    |  | |  | |||  |   |   ||||   |   |  ||   ||  ||   | |  |||  | ||     |||| ||| | |   | |  | | ||||||  |||||||| || || ||||| ||||||||||| |||||||| |||||||| || || || || ||  | || || |||||||| ||||| || 
----------------------------------------------------gtatccataaatatttcatacttta-atttttaagttgattatcatcataatagaatgtgatt-ttatgtaacattcaatgtgttggtttgttcattgattcaattaagtgtttaccttacata--tgttatcttcaagTTTGAATTCCACCATTGTGCCATTATTCGAGAAGGTTCTGAGTGCTAGTGATGCTGGTCGAATTGGTCGTTTGGTCCTCCCAAAAGCATGTGCTGAA

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|5268958|gb|AI770922.1|AI770922

EST:     CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGAGA
genomic: CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA

EST: gi|67040653|gb|CO466908.1|CO466908

EST:     CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
genomic: CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA

EST: gi|13150757|gb|BG321079.1|BG321079

EST:     AACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTSA
genomic: AACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA

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), 46 (downstream exon)
Score: 106

GTGTTGCTAGGCCACCTGCTGAAGGAAGGGGCCGCAATCAATTACTTCCTCGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 215

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG