ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgacaccttcactcatgtaccataactcttatctaaagacctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG

Basic information

species	Zea mays
transcript	GRMZM2G058870_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g14260.1 (Oryza sativa), 3'ss of exon 8

gtatgacaccttcact------catgtaccataactcttatctaaagacc--tctgcaacattcttgttttcagtcctgaacatggattgccggtt-tacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
|||||  | ||| |||      |||||||| | | | |||  |  |||    ||||     ||    |  | |   ||||  || ||||    | |  | || |||||||||||||| ||||| ||||||||||| || ||||||||||||||  |||| ||||||||||| || |||||||||||||| |||||||| ||||||||||
gtatggaatctttacttgcacccatgtaccttgatttttacatgtagattgttctggtttgtttcattccttatctctgagtattgattatttgctacatatttttcagGTCTTTGCAACAGCTTCATATGATGACCATAAAAATATTGTACTCCTGGCGTTTGAAATTATCGAGAAGATTTTGCGGGAGTACTTTCCCTACATTACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 9

----gtatgacac-cttcactcatgtaccataactcttatctaaagacctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatc-tttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
       ||| |  || |  |  | ||     |   | |  ||| | | | ||     ||| | |||||  ||||  || |  | |||   |  |  |  |||||||| ||  | |||||  | |||||||| |||||||| |||||||| ||  | ||||||||||| || |||||| | || || |||||||||||||| ||||
gtagagctgataaactcctattgtctatagagagcttcaattaatg-catatgtt-tgttcattttttctctcctctactt--actgctcatagatctgatttcagGTATTCACAACAGCAGCTTATGATGACCACAAAAACATTGTACTCTTATCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATACATCACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 8

----gtatgacac-cttcactcatgtaccataactcttatctaaag---acctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
       ||| |  || |  |  | ||     |   | |  ||| |   |  | ||    ||| || | | |    ||    || | |    |   |     |||||||| ||  |  ||||  | |||||||| |||||||| |||||||| ||||| ||||||||||| || |||||| | || || |||||||||||||| ||||
gtagagctgataaactcctattgtctatagagagcttcaattaatgctaatgtttgtgg-atttttttctcctcctctacttattgctcatagacctg---atttcagGTATTCACAGCAGCAGCTTATGATGACCACAAAAACATTGTACTCTTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATACATCACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G45360.1 (Glycine max), 3'ss of exon 10

------gtatgacaccttcactcatgtaccataactcttatctaaagacct-----ctgcaacattcttgttttcagtcctgaacatggattgccggtttacatc-tttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
       ||    |  |||  |   |  |   || |   ||  |||    |     ||||   | | ||  ||||| |  |    |   |||||  ||  ||||  || ||||  ||  | |||||  |||||||||| |||||||| |||||||| ||||| ||||||||||| || |||||| | || || ||||||||  |||| ||||
gtagggctaatttatgttccatagagggcttcaatttgcatggaaaatgtttttgtctgccgaagtttttctttca-ttatttctactcattgcttgtggacataattccagGCATTCACAACAGCAGCATATGATGACCACAAAAACATTGTACTCTTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCTCACATCACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 8

gtatgacaccttcactcatgtaccata-actcttatctaaagacctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatc-tttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
|||   |   |  |||| | |    || |     ||  ||  |   |       |  |  ||||   ||      |   | |||   |  || |  |||||||| ||  | |||||  | |||||||| |||||||| |||||||| || || ||||||||||| || |||||| | || || |||||||||||||| ||||
gtaaagctgataaactcctattgtctatagagagattcaattaatgcaaatgtttgttcattttttctctcctctacttactgctcatagacctgatttcagGTATTCACAACAGCAGCTTATGATGACCACAAAAACATTGTACTCTTAGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATACATCACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 8

gtatgac-accttcactcatgta-----ccataactcttatctaaa--------gacctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
||| | | |  |||  |   |||     |   || |   ||  |||        | |  ||| |   ||  | |  | | | ||   ||| | |||  |  |||    || ||||| ||  | |||||| |||||||||| |||||||| ||||||||  |||| ||||||||||| || |||||| | || || |||||||||| ||| ||||
gtagggctaatttctgttccgtagagggcttcaatttgcatggaaaatgtttttgtctgctgaagtttttctttcattatttctactcattgcttgtggactta---attccagGTATTCACAACAGCGGCATATGATGACCACAAAAACATTGTACTCCTGGCTTTTGAAATTATGGAGAAGATTATTCGAGATTACTTTCCATGCATCACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 8

gtatgacaccttcactcatgtaccataactcttatctaaagacctctgcaacattcttgttttcagtcctgaacatggattgccggtttacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
             |  ||| ||   ||| |    |||    ||| |   ||  |     ||||  |   |   ||     ||     || | |  | ||||| ||| | |||||| ||||||| || ||||||||||||||  | ||| ||||||||||||| || |||||| | || ||||| || |||||||| ||||
-----------gtaggcatttattgtaattt---tctggtaaccacattaatttaagaattttttggtttactcacaatgtgttttcttccgt--tgcagGTTTTTACCACAGCGGCATATGACGACCACAAAAATATTGTGTTTTTGTCCTTTGAAATTATCGAGAAGATTATTCGAGAATATTTCCCATACATCACTG

upper sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 8

---------------------------------------gtatgacaccttcactcatgtaccataactctt--atctaaagacctctgcaacattctt--gttttcagtcctgaacatggattgccggtttacat----ctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG
                                        |||| ||  |       || |   ||  ||||  || | |   | ||    |  || ||  ||     |   ||   |  ||||     | |  ||     |||||||||||  | |||||  | ||||||||||| ||||| || |||||  ||||||||||||| || || |||||| |||| || ||||| || ||||||||||
gtattgaaatctgtccaatctgtagttttctattaaagaatatg-caagtgagggagtg-attttagttcttcaatttgatttcatcattgattttatttggtgaatggctatgttaacagattattaatgtgaatatttttttcagGTCTTCACAACAGCAGCTTATGATGATCATAAAAACATAGTACTCCTGGCCTTTGAAATAATTGAGAAGATTGTGCGAGACTACTTCCCCTACATTACTG

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: 551

CCGAGCTGTTGAGATCAGAGAACTTATCATTAGGTGTGTCTCTCAAATGGTATTGGCCCGTGTTAGTCATGTGAAGTCAGGGTGGAAGAGTATGTTTATGgtatgacacc ... catctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 368

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 785

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgcaacattcttgttttcagtcctgaacatggattgccggtttacatctttcagGTCTTTGCGACAGCGTCATATGATGATCACAAAAATATTGTACTATTGGCCTTTGAAATTATAGAAAAGATTTTGCGGGAATACTTTCCATACATTACTG

                                             catctttc  CT-rich tract
           ttgtttt  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

RNA-Seq data