ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

Basic information

species	Zea mays
transcript	GRMZM2G004040_T01
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2

gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
     |  |   |||||  | ||  || || |||    ||  || ||||||| | | |  || || | |||||| ||        ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||||
-----gtaaccttatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgatttt-------gcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT

upper sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2

gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatc-ttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
                 | |  | ||| ||      || |  |    ||  ||||  | | |      ||| ||  ||||||||   ||||||||||  |||||||||||||||||||||| || |||||||| || ||  | || || ||||| ||||||||| |||||
----------------gtatctttgaacagtttggagtgca-attcgttcctctggttttagaaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT

upper sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 10

gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatc-ttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
                 | |  | ||| ||      || |  |    ||  ||||  | | |      ||| ||  ||||||||   ||||||||||  | |||||||||||||||||||| || |||||||| || ||  | || || ||||| ||||||||| |||||
----------------gtatctttgaacagcttggagtgca-atttgttcctctggttttagaaattgattcattattttatcttctagGGAATAATATTAATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACGAGGCCTGGCAGATTTGATCGGCAT

upper sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10

gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
    |  || |  |   | | | |   |       | || | ||   | | ||||  || |  ||           |||||||   |||||||||| || || |||||||||||| |||| || ||||||||||| ||  | ||||| ||||||||||||||||| |||
---gta-tatttcaagttttaaacatttgtgagtgtttaattagt-ttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT

upper sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10

-----------gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
             |    |||| |||| ||||||    |   | | | | |  || | | ||   |    |||||| | |||     ||  |    ||||||||||| || |||||||||||||||||||| || || |||||||| || || |||||||| |||||||||||||| |||
gtacttgttgattaggagtagtgtatcttgtgattacttccgctagtttgc--aggaatataatagtactttgctttctatt-----ttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT

upper sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 10

gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT
            || ||| ||  | ||          || | |  | |||     | | ||    |      |   ||| |||   |||| |||||  ||||||| |||||||||||||| || ||||||||||| ||  | |||||||||||||||||||| ||||||
-----------gtaacatatggacaaacttgtgttattagtgaatatttttctgcatttttttaacttggataatatttttcttgtagGGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCAT

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: 43 (upstream exon), 46 (downstream exon)
Score: 78

AATAGATGCTGTGGGATCAACTAGGAAACAGTGGGAAGGGCACACAAAGAAGACATTGCATCAACTTCTTGTTGAGATGGATGGGTTTGAACAAAATGAGgcaatgctag ... tatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 100

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 54

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

                                        tcttttatctc  CT-rich tract
                                  aattgatcttttat  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

RNA-Seq data