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

...acagtgcccgtttatttgtgttttataggcaaaacaacatgttgacattgacatcatttgagaaaaaaaaacaatgtctgatcgtgtatcacttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAACCCGAGGAGTCACGGCCATACAGCAGGCCGCAGTCCACGTCTGAGTACG

Basic information

species	Zea mays
transcript	GRMZM2G155662_T03
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G155662_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g05350.1 (Oryza sativa), 3'ss of exon 5

-----acagtgcccgtttatttgtgttttataggcaaaacaacatgttgacattgacatcatttgagaaaaaaaaacaatgtctgatcgtgtatcacttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAACCCGAGGAGTCACGGCCATACAGCAGGCCGCAGTCCACGTCTGAGTACG
       | ||   | || | | | | || || | |||  |||||   ||  |      |||    ||||  ||  |   ||   |   |   |  |   ||||||| |||||||| || || ||||||||||||||||||  || ||| || ||||| || || |||||| | ||||  ||||| || |||  | |||| || |
gttaagaaatgaatgcttttctttttatt-tacgtaaa-taacatacagaagtcatatccatgcttgaaactaatgcccagttacacttt---ttgcacctgcagTATATCATACCACATCTTATGGGCTGGAGCACATTTACAAATTCTATAAAACCTGAAGATTCACGGGCGTACACTAGGCCACAATCCGGGCCTGAATATG

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|89247406|gb|DY619192.1|DY619192

EST:     ATTGTATTAACTTTCAAT                         TACATCATACCGCACCTCATGGGCGGGAGCACATTTGTAAGTTCAATCAAA
genomic: ATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

EST: gi|76019635|gb|DT946805.1|DT946805

EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

EST: gi|78075430|gb|DV503864.1|DV503864

EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

EST: gi|89247469|gb|DY619255.1|DY619255

EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

EST: gi|93015158|gb|EB640678.1|EB640678

EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

EST: gi|71325426|gb|DR799397.1|DR799397

EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

EST: gi|213179367|gb|FM192339.1|FM192339

EST:     ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAAT                         TACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA
genomic: ACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAA

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: 45 (upstream exon), 47 (downstream exon)
Score: 43

ATGGCTGCTAGGTGTCCAGAATCGGCTTATCAACGTTGATGAGAGCATTTACATCCCTATAACCAAGGGAGAGTTTGCTGTCATTGTATCAACTTTCAATgtaagtagca ... acttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAACCCGAGGAGTCACGGCCATACAGCAGGCCGCAGTCCACGTCTGAGTACG

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 62

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 20

Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 22

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cattgacatcatttgagaaaaaaaaacaatgtctgatcgtgtatcacttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAACCCGAGGAGTCACGGCCATACAGCAGGCCGCAGTCCACGTCTGAGTACG

                              gtctgat  putative branch site (score: 22)
          atttgagaaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtgcccgtttatttgtgttttataggcaaaacaacatgttgacattgacatcatttgagaaaaaaaaacaatgtctgatcgtgtatcacttgtgcagTACATCATACCGCACCTCATGGGCTGGAGCACATTTGTAAGTTCAATCAAACCCGAGGAGTCACGGCCATACAGCAGGCCGCAGTCCACGTCTGAGTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG