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

gtatgttcccgagccacccagcaacgcttgcttttaatgcattgatgctaatcctatccgatagtggctgaggagtattttttttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG

Basic information

species	Zea mays
transcript	GRMZM2G130348_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G130348_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g17390.1 (Oryza sativa), 3'ss of exon 3

gtatgttcccgagccacccagcaacgc--ttgcttttaatg--------------------cattg-----------atgctaatcctatccgatagtggctgaggagtattttttttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG
|||||||||||||| ||||| ||||||   ||||||  |                      ||||            ||||||||| |||| |||||||  |||||||||||||       | ||||||| |||||||||  |||||||   | | |||    |||||||||||||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||| ||||||||||
gtatgttcccgagc-acccaacaacgcaaatgctttggacagtgctagaagaaccaataaacatttccatatgggatatgctaatcttatctgatagtga-tgaggagtatttt-------accagtggacagtgtgttc--attcatgtgttgctatg----tttggcagGCTGGTGGTATGGAGTTGTTGGCCACTTGGAGTCATGTGATGGAAGTGAGCACTTTTGTCGGTGTCATCTTAGTG

upper sequence: GRMZM2G130348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G08260.1 (Glycine max), 3'ss of exon 3

gtatgttcccgagccacccagcaacgcttgcttttaatgcattgatgctaatcctatccgatagtggctgaggagtattttttttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG
                           |   |||  || | || ||  ||    ||||   ||   | |  | | ||| ||    | ||    || || || ||          ||||| |  |        ||||||| ||||||||||| ||||| || ||||||||||||||  |||| || ||| | | ||| || || |||  |||||
-------------------------attaattttatatac-ttcatattagaagtatcaagtatatgattggaaatatattaagctaaa---atgaattgt-tgcatgacgaggtgcaccttta--------tggcagGTTGGTGGTATGGTGTTGTAGGCCACTTGGAGTCATGCAATGGGAGTGAAAATTATTGCCGATGTCATAGTAGTG

upper sequence: GRMZM2G130348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G36360.1 (Glycine max), 3'ss of exon 3

gtatgttcccgagccacccagcaacgcttgcttttaatgcattgatgctaatcctatccgatagtggctgaggagtattttttttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG
                            || |   |  || ||  |     || |||  || |||   |||   | ||| |       || |    | | ||  || |    ||||          | | | ||||||||||||||||||| ||||| || ||||||||||||||  |||| || ||| | | ||| || || |||  |||||
----------------------------tgataaaagagcctttgtatacttcatattaga-agtacatgattggaattat-------attaagctaaaatgaattgttg--catgacgaggtgcacctttatggcagGCTGGTGGTATGGTGTTGTAGGCCACTTGGAGTCATGCAATGGGAGTGAAAATTATTGCCGATGTCATAGTAGTG

upper sequence: GRMZM2G130348_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G04080.1 (Glycine max), 3'ss of exon 3

gtatgttcccgagccacccagcaacgcttgcttttaatgcattgatgctaatcctatccgatagtggctgaggagtattttttttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG
                   |  ||   || ||| |      || ||  |     | ||| |||    ||      ||   ||||||     ||| ||| |  ||         |||||| |  |        ||||||| ||||||||||| ||||| || |||||||||| ||| ||||| |  ||| | |  || || || |||  |||||
-----------------ataaaaataattacttctccaatcttaattatg-cattttcctata-catctatc---tacccttttttgtgatagtagattg-atgaa-------atgcaccttta--------tggcagGTTGGTGGTATGGTGTTGTAGGCCACTTGGAGTTATGCGATGGGAATGAAAATTACTGCCGTTGTCATAGTAGTG

upper sequence: GRMZM2G130348_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ30849 (Selaginella moellendorffii), 3'ss of exon 3

gtatgttcccgagccacccagcaacgcttgcttttaatgcattgatgctaatcctatccgatagtggctgaggagtattttttttttaatc-agtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGT------GATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG---------
                                                                  |     |    | ||| ||||  || || ||||| |    | | |  || |   ||   | | | | |||||||||||||||||||| ||||||| ||||  || ||||||      |  || |   |   |  | ||| |     |  | |           
------------------------------------------------------------------gtatgtgttcctgtttgttttgctcgagcggata-taaact-taagacaagtttttgttttc-tatctggcagGCTGGTGGTATGGAATTGTTGGTCACTCTGATTCATGTTCCAACGCCGGGAATAATAGCAGTCGTCAGCATTGTTCTTGCCAGAGTGACA

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|149000598|gb|EE037796.2|EE037796

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

EST: gi|149009737|gb|EE154079.2|EE154079

EST:     GCGACCACATCGAGATTCAGTGGAGAAAGGAACAAAGAATTCCCCATACC                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCAAA
genomic: GCGACCACATCGAGATTCAGTGGAGAA-GGAACAAAGAATTCCC-ATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAA

EST: gi|6012313|gb|AW061669.1|AW061669

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

EST: gi|21331057|gb|BQ486438.1|BQ486438

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

EST: gi|76013482|gb|DT940652.1|DT940652

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

EST: gi|26455381|gb|CA826964.1|CA826964

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

EST: gi|14203843|gb|BG837520.1|BG837520

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

EST: gi|71771777|gb|DR969714.1|DR969714

EST:     CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACG                         GCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC
genomic: CGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAAC

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), 48 (downstream exon)
Score: 63

ACCCTTGCGCATGACCTGCACACCTCTGACTGCCTGCATGAGCTCCGGCCCGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttccc ... tgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 61

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 29

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG

 ttttaat  putative branch site (score: 29)

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcccgagccacccagcaacgcttgcttttaatgcattgatgctaatcctatccgatagtggctgaggagtattttttttttaatcagtggatagtgtgttctcattcatgcacttccatgcatgtttggcagGCTGGTGGTATGGAGTTGTTGGGCACTTGGAGTCATGTGATGGAAGCGAACACTTTTGTCGGTGCCATCTTAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG