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

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

Basic information

species	Zea mays
transcript	GRMZM2G076826_T04
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g53240.2 (Oryza sativa), 3'ss of exon 6

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcct--cacttgatcttacttgcatt-ctcacttgattttactt----gcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                        | |  |   ||| ||  ||||| |||   | |   |  ||      |||   || ||       |||| |     ||||    |  | |    || |||||   |||  | || | | ||     |||   || |  ||  ||||||||||||||||  |||| || || |||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||||  |  
-------------------gtctgaaaatcccttgaatc--attttcctttgaaaacacaaggactttggtcgaatagtatactactgcatggtttatgatcccagtatctcaaagaacctgcatggttcatgttatctcatttcatcactttgttggatttg--cagCTGCTCTGATGTCCGCAATTTACGAGGAGAACAAGGATGAGGATGGGTTCCTCTACATGACCTACAGTGGCGAGAACACCTTTGGGCTGCTCTAGGCGCG

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 5

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgctt---ccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                                                      | ||||   ||  | |   || |  |||     |||     |       |   ||     ||  |   || | | ||   || | ||  ||      ||        |||||||  |||||||| | |||||||| || ||||| ||||||||||| ||||| || ||||| |||||||| || ||||| || ||     ||||   |  
-----------------------------------------------------gtgagaaagaattcctt---tttaatattcaaatacacatatcgatgatgtagttt--ctgtaactat-ttattatttatattcatttatttgtattttgtgttatcacagCTGCCATGATGTCTGCCATCTATGAGGAAAACAAAGATGAGGATGGTTTCCTGTATATGACTTACAGTGGGGAAAACACATTTGGATCATTCTAACGGAA

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttg-agcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC-
                                                     |  ||       | |   || ||  |||      | | || | | || ||      |   || ||   | | ||  |  |    | |||||  |||  |  |    |||| || || ||||| || |||||||| ||  ||||||||||||| || || || ||||| |||||||| || |||||||| |||||   ||        || 
----------------------------------------------------cagcagggccagagccgggcgctgtggcacc----gccgtg-tgcaccgtcgctgtctttgctcacc-acgtccttgc--gcccctccttgcaaccc--actcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG-TGCCGGGGAGCAGCT

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4

---------------gtctg-gaaaataaatacagagacaacatacttctgactctgattttgc----------ttcctataagaa--ttgatggcattcgttgagcatt-tggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctg--tgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC
                |  | | || | |||  ||          ||| ||  |  |||||||           ||   ||   ||  |||  | | |  |    ||| |  |  ||  || |      |   ||||    |  |  ||     | | |  | |  |     |     | |  ||  |||||| ||| ||||||| || |||||||| ||| ||||||| || || || ||||| ||  | |||||||| ||||||||||| ||||||||      |||   
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtg-gcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactg---cagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S249_49V6.1 (Physcomitrella patens), 3'ss of exon 4

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGG-GCTCCTCTAGATGGC
                                       ||||| |  |   | ||  | |  |  ||  | ||   | |||||  ||   | | |   ||  ||| |  || |  |         || |  | |||  |||              |||||||||| ||||||| || || || || ||  ||||||||||||| |||||||| ||| | || ||||||||||| ||||||||||| | |  | |  |  | 
--------------------------------------ttgattctagtctgtgtattattgcactgctgttgtgtgggatttgttgatgggttacttaat--tcattgaatgtcgcac-------cattcaactttgtttg--------------tgcagCTGCTATGATGTCATCCATTTACGATGAACACAAGGATGAGGACGGATTCCTGTACTTTACTTACAGTGGTGAAAACACCTTCGGAGATGTTATCAACTG-

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 4

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC--
                                                                                         ||||    || ||   || | |||  || |  ||       ||||||    || | |  |   | | || ||| ||  |||| ||  | ||||| || ||| ||||||| |||||||||||||||||| | || ||||| || ||||| ||||||||   |    |||   |  
---------------------------------------------------------------------------------------gtatgag---ccgtcgagacgtaatcccacgtatat-------tgatttacactgttcctttc--cttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG--CCAAGAAGAACACTA

upper sequence: GRMZM2G076826_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 4

gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC--
                                                                                         ||||    || ||   || | |||  || |  ||       ||||||    |  | |  |   | | || ||| ||  |||| ||  | ||||| || ||| ||||||| |||||||||||||||||| | || ||||| || ||||| ||||||||   |    |||   |  
---------------------------------------------------------------------------------------gtatgag---ccgtcgagacgtaatcccacgtatat-------tgatttacactattcctttc--cttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG--CCAAGAAGAACACTA

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|91052589|gb|EB163007.1|EB163007

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|17931727|gb|BM268687.1|BM268687

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|91052588|gb|EB163006.1|EB163006

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCCCCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|211515507|gb|FL476344.1|FL476344

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|18174937|gb|BM350325.1|BM350325

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|18169711|gb|BM339551.1|BM339551

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|16918829|gb|BM073915.1|BM073915

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|16926343|gb|BM079411.1|BM079411

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|17930090|gb|BM267050.1|BM267050

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

EST: gi|93016973|gb|EB642493.1|EB642493

EST:     TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCCCCAACAG                         CTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC
genomic: TGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCC

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: 315

CTTACGGTTGGACAATTCGTGTATGTTGTTAGGAAGAGAATCAAGCTCAGTGCTGAGAAAGCTATCTTCATCTTTGTGAAGAACACCCTTCCACCAACAGgtctggaaaa ... acctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 459

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 495

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 507

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

                       ttgatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggaaaataaatacagagacaacatacttctgactctgattttgcttcctataagaattgatggcattcgttgagcatttggggacatgatcccccatcctcacttgatcttacttgcattctcacttgattttacttgcttccctgaacctgtgcagCTGCTCTGATGTCTTCAATCTATGAAGAGAACAAGGATGAGGATGGATTCCTCTACATGACCTACAGTGGTGAGAACACCTTCGGGCTCCTCTAGATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC