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

gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA

Basic information

species	Zea mays
transcript	GRMZM2G430027_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 3'ss of exon 18

gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgtt-gagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
               | | | |||||  |||  | ||| ||||  |  | | |   |||  |       |       ||| |     | | |||| |||||| |||||||| |||||||| ||||| ||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||| ||  ||||| |||| || ||||
--------------gtatgattgtttaattg-tttacagtgca--acgtatgatgctatattcctaacttccac--agctaac----attttttttcctgtttgagcagCACGAGGAAAGTGCGATTGAAGAGCTTGCTAGGGATTACAATGCAAACTGGATGAGTGCAGTTGAGATGCTTGATGACGAGATCTATATTGGAGCAGAGA

upper sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 18

----------gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgttgagc----agCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
           ||| |      || |||  | || |  ||   | |         |  | | | ||| || ||| |        |   | || |  |    || ||  ||||        |||| |||||| | |||||||| ||| | ||| |||| || ||||||||||||||||| ||||||||||| ||  |||||||  ||||  | ||  | || |
gtaaaacgttttggatacgaaattgtttttccgtct--ttatatgaatacatgccaaatcttagattgttatgttcacaagaactcaccggactcttttgattatctgtgtttgttttaaagCACGAGGAAGGTGCGATCGAGGAGAGAGCTCGGGACTATAATGCAAACTGGATGACGGCAGTTGAGATACTCAATGATGACATCTACCTCGGTACTGATA

upper sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G05420.1 (Arabidopsis thaliana), 3'ss of exon 18

gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctt-tgttggg-ctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
               | |||||  | |    | |     ||  |||       |  || | ||| | | |  | |||   ||||| ||| || | ||   |||  |  |||| |||||| | || || || ||||| ||| |||||||||||||||| |||||| | || |||||||| || ||||||||  | ||  | || || ||||
--------------gtataacttctagacgaaatttgtgtgt-ttaaaaactgatctactatgttcatttggtattgtttctgatggcttat-tcttgaatgtaaa--agCACGAGGAAGGTGCAATTGAGGAGCGGGCTCGGGATTACAATGCAAATTGGATGTCAGCGGTTGAGATACTCGATGATGATATTTACCTCGGTGCTGAGA

upper sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 18

----------------gtgggtgacgggttttttaactgtttgcttgactcacattgcatt-atctgtaaaattattgtgtccgtct-------ttgttgggctgattgctaatgttt------tccctgttgag----cagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
                    || |    || |     ||   ||  |  |  | || | |  |  |  || | | ||||||  || |       || | |   || |     |||| |      ||| | ||       |||||||||||| | || || |||||||| ||  | || ||||||||||| |||||| | || |||||||| |||||||||||  | ||  |||| || ||||
gtaagatgactaatcttcaagtaatcccttgtccttttggcagcaagtatggcgttccctggagttaaaagagtgttgtgtttgtttgttactcttatcgtcttgttaatggatgtctgattggtcctttttttattttcagCATGAGGAAGGTGCCATTGAAGAGCGAGCCCGTGACTACAATGCAAATTGGATGTCAGCTGTTGAGATTCTTGATGATGACATTTACCTTGGTGCTGAGA

upper sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ23079 (Selaginella moellendorffii), 3'ss of exon 18

gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
                                                 |||   |  ||||        || |   ||| || |  | |||||   ||  |   ||||  |||||| | ||||||||||| || ||  |||||||||| ||||||||||||||||| || ||||| || || || ||  ||||  | || || ||||
-------------------------------------------------gtatgctctttgtacagagtgttttcttgcttatgg--actgttta--ctacttcacagCCGGAGGAAGGAGCGATCGAAGAACGCGCGCGGGATTACAACGCAAACTGGATGACTGCTGTGGAGATCCTGGACGACGACATCTACCTCGGAGCCGAGA

upper sequence: GRMZM2G430027_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ30457 (Selaginella moellendorffii), 3'ss of exon 18

gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA
                                        | ||  |||    |   | ||| | | |  || | |  ||| || |||     |||         ||||  |||||| | ||||||||||| || ||  |||||||||| ||||||||||||||||| || ||||| || || || ||  ||||  | || || ||||
----------------------------------------gtatgctcttcgtagagagtgttttcttgcttat-gaactgtttacta----cttc--------acagCCGGAGGAAGGAGCGATCGAAGAACGCGCGCGGGATTACAACGCAAACTGGATGACTGCTGTGGAGATCCTGGACGACGACATCTACCTCGGAGCCGAGA

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|211183657|gb|FL219825.1|FL219825

EST:     TCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAGgtgggtgacg ... tgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG

EST: gi|5566749|gb|AI881615.1|AI881615

EST:     TCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAGgtgggtgacg ... tgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG

EST: gi|44900212|gb|CK826757.1|CK826757

EST:     TTGGCGATCTGATGAAGTCAA-TTCCCTGCTGGGTGTATAAG                         CATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TTGGCGATCTGATGAAGTCAATTTCCTTGCT-GGTGTATAAGgtgggtgacg ... tgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG

EST: gi|32836031|gb|CD975709.1|CD975709

EST:     TCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAG                         CATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG
genomic: TCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAGgtgggtgacg ... tgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGG

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: 46 (upstream exon), 48 (downstream exon)
Score: 156

TGGCCACCATGGGCACATACTTGCCTTGTACACTCAAACACGTGGTGACTTCATTGTGGTTGGCGATCTGATGAAGTCAATTTCCTTGCTGGTGTATAAGgtgggtgacg ... tgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 66

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aattattgtgtccgtctttgttgggctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA

                              tgctaat  putative branch site (score: 59)
                                      ttttccctgtt  CT-rich tract
                                 taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgacgggttttttaactgtttgcttgactcacattgcattatctgtaaaattattgtgtccgtctttgttgggctgattgctaatgttttccctgttgagcagCATGAGGAAAGCGCGATCGAAGAGCGTGCTAGGGATTACAATGCAAACTGGATGACTGCAGTTGAGATGCTTGATGATGAAGTCTATGTTGGGGCGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG