ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

Basic information

species	Zea mays
transcript	GRMZM2G000645_T02
intron #	15
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 15

gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgc-ttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
||| |||| || ||||| |    |    || | |||        | |    | | ||  | |  |    |    |||  |||| | ||||   | | || | ||||||||||| || |||||||| |||||||||||||||||||||||||||||| | ||||| ||||| ||||||||||||||||||||||| || ||
gtatatattgtgtgctccatgcaagaatttttattt--------tgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15

------------------------------------------gtaaatatagt-ctgctcgaaaacatttcttct----gtt--taaattctctatatgggcacttcatgt----catgacttcaattgcttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                                           ||  ||| |  ||  | |  | ||| | ||||    |||  | ||||   ||||||   | ||  ||     || |  |   |    |    | | |  |   | ||||   |  |||| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 15

--gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgctt-acatagt----tataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
   | ||     |   ||   | |  | |  | |    ||    | |  ||      || ||   |  ||    ||      ||||  |     ||||   ||||   |  |||| ||||| |||| ||||||||| ||||| |||||||||||||||||| |||| ||||||||||| |||||| | |||||||| ||||| ||
gtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 4

------------------------------------------gtaaatatagtctgctcgaaaa-catttcttctgttt------aaattctctatatgggcacttcatgt----catgacttcaattgcttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                                           ||  ||| |    ||||  || ||| | |||| | |       ||||   ||||||   | ||  ||     || |  |   |    |    | |||  |   | ||||   |  |||| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||
gtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATAGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 15

---gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcact--tcatgtcatgacttcaattgcttacatagttataagct--ttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
    ||| | |  ||   || | |    |  ||      ||    | |  ||      |  |      | ||     ||     |  | | || |   |  ||||   |  |||| ||||| |||| ||||||||| |||||||||||||||||||||||| |||| ||||||||||| |||||| | |||||||| ||||| ||
gtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatttagGTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 19

gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatggg-cacttcatgtcatgacttcaattgcttacatagtt--ataagctttatac-ttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                       |   ||  | | ||  || |    | |   |  || ||||  |   ||   |||         ||   ||  | |  ||  |||||||| ||||||||||||||| |||| || ||||||||||||||||| ||| | || || |||||  | |||||| | |||||||| ||||| ||
---------------------gtaaggctcatttctaggtttttggaaagaaacgttttatgttttttattttgttgtaattgagattcagtactcctcttatattacagGTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15

gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
            | ||| | |   | | ||   ||  |||  ||| |||| ||  | |||   || |    |  |||| | |||  | |              ||||| || ||||||||||||||||| ||||| ||||| ||||| || |||||||| |||||||| || |||||  |  | ||||| || || ||
-----------gtactcaagagtctatttttatttctaatcatctttatgagc--tacattatataa---tagctgctaatatacctgtgg------------cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15

gtaaatatagtctgctcgaaaacatttcttctgtttaaatt-ctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
                     |   | | | | | |   || ||||   | || | ||   || ||||  |  |||      || |||   | | |  || |   |||| || ||||||||||||||||| ||||| ||||| |||||||||||| |||| |  |||||||| ||||   |  | ||||| || || ||
-------------------gtattgtgcatatatgttggttactctgatttggaagtt---gttatgaactggattctaatgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 15

gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtc-atgacttcaattgcttaca------tagttata-agctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
     ||| || |  | |   ||  || |  ||     ||| || ||||| |||  | || || ||  | |  ||| |||  |      | |||| | | |  |||  |  ||||| || ||||||| ||||||||| || |||||||| |||||||||||| | || || ||||| || || ||||| || ||||| ||||| ||
----gtattgtgta-ttgtccacccttgtcttgaaagtatt-tccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccatatgttc-cagGTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15

gtaaatatagtctgctcgaaaacatttcttct--gtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA
             |    | |   ||  |||   |||  | |||| |||||  |  ||||||   | |  | || |    ||   | || | |   | ||  || ||||| || || |||| ||| ||||| || |||||||| ||||| |||||| |||| |  |||||||| ||||||||||| ||||| ||||| ||
-------------gtataagagagttgattccaggttgtatttctatatatatgatcttcattctaagg-tgcagtcatata---aattgttaatgtgatgatttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA

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|18965038|gb|BM661357.1|BM661357

EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT

EST: gi|19351531|gb|BM896063.1|BM896063

EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT

EST: gi|89106492|gb|DY576709.1|DY576709

EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT

EST: gi|22490520|gb|BU050443.1|BU050443

EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT

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: 48 (upstream exon), 49 (downstream exon)
Score: 195

TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 74

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

                       tgcttac  putative branch site (score: 177)
                          ttacatagttataa  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG