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

gtaattcagttattaaatatttatgtggttgttggtgaatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC

Basic information

species	Zea mays
transcript	GRMZM2G022563_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g55060.1 (Oryza sativa), 3'ss of exon 4

gtaattcagttattaaatatttatgtggttgttggtgaatcatactctca----aaattaatat-gtcac-----ttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC
|||| ||  || ||     ||     | |||||||  | ||| || ||||    |  ||  | | |||||     | || ||||||||| | | ||| ||||| |||||  | | |||| |  ||||||||||||| |||||||||||| |||  ||||||||||||||||||||||||||||| || ||||||||||||||
gtaactcttttttttttccttgtgaggattgttggcta-tcaaacactcacaggaggttgttgttgtcaccttgttcgattaatatatg-acaatttcgtagGTGGAGGCATCCGGAATATTCTAGTAATTGGTGCCGATGCTCTTTCACAATTTGTGGATTGGACAGACAGAGGTACATGCATCCTCTTTGGTGATGCTGC

upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G41380.1 (Glycine max), 3'ss of exon 4

gtaattcagttattaaatatttatgtggttgttggtgaatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC
       |   |||   ||||| ||| ||  ||| | | || ||      |  || | |  ||| |||     ||| ||  |   ||   ||| || || ||| | |||||  |||| ||||| || ||||||||||||  ||| || ||||||||||||||||| || || ||||||||||| ||||||||
-----gtatgaattggctatttttgttgtc-ttgataattcctaaat---atgttga-aaatca-ttgccctttat-tgtgtgagttc--agGAGGTGGGTTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTTTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGC

upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G44350.1 (Glycine max), 3'ss of exon 4

gtaattcagttattaaatatttatgtggttgttggtgaatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC-
          ||| || |  |||| |  ||||  |      |    || || ||    |      |||     |||     |     || ||| || || ||| | |||||  |||| ||||| || |||||||| |||  ||| || ||||||||||||||||| || || ||||||||||| |||||||| 
----------tatgaattggttattt--ttgtcagcttgatagttcctaaatatggggaaaatcattgccctttat---tgtgtgaatgcaggAGGTGGATTTAATAATGTTCTAGTTATTGGGGCGGATGCTCTCTCACGATATGTTGATTGGACAGACAGAGGGACCTGTATTCTTTTTGGGGATGCTGCT

upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S11_305V6.1 (Physcomitrella patens), 3'ss of exon 6

----gtaattcagttat--taaatatttatgtggttgttggtgaatcatactctcaaaattaatat-gtcacttgaa-taatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC
     || ||  ||  |  |||  | |    | |   |   | ||         | ||   ||  | ||| | | ||   | || || |    | || ||| || ||||   | |||||  | ||  ||||| | ||||||||||||| ||||||||||||||| || ||||| || || || || |||||||||||| |
tgttatatttttgtcttcctaagcaatcgaattgagttctttcaacttggtaaaccaatcgaaagttgtctcctaaagctaaatttgaaggtgtgtgcagGAGGTGGTTACGAAAATGTTCTTGTGGTTGGTTCTGATGCTCTTTCAAGATACGTGGATTGGACGGATAGAGGAACGTGTATCCTATTTGGTGATGCTTC

upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S119_22V6.2 (Physcomitrella patens), 3'ss of exon 6

--gtaattcagtta--ttaaatatttatgtggttgttggtgaatcatactctcaaaatta-at-atgtcacttgaataata-----tatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC
  | || | |||    | |||  |  |  |  ||  |  |  ||| ||||   | ||| | || ||||    ||  ||| |     |  | |    | || ||| |||||||   |||||||  | ||  | ||||| |||||||| ||   ||||||||||||||| |||||||| ||||| ||||| ||||| |||||  |
gggaaactaagtccactgaaaggtgcacttaattcatcct--atc-tacttagagaatcacatgatgttggctgtctaaaactaacttcgaaagtgtgtgcagGAGGAGGTTACAAGAATGTACTTGTGGTGGGTGCGGATGCTCTATCGCGATACGTGGATTGGACTGACAGAGGGACATGTATTCTGTTTGGCGATGCCTC

upper sequence: GRMZM2G022563_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S87_63V6.1 (Physcomitrella patens), 3'ss of exon 6

-gtaattcagttattaaatatttatgtg-gttgttggtgaatcatactctcaaaattaat--at----gtcacttgaa--taatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC
    ||   || |||   | | | |||  |  |||    | | | | | | |||   ||   ||    | ||||| ||  ||| || || |      || ||| ||||| | ||| |||||  | ||  | ||||| || ||||| |||| ||||||||||||||| |||||||| || || ||||| ||||| |||||  |
tcgcatgttgtaattgg-tgtctttgtaagcagtttaacacttaaaatttgaaagccaactgatagcggccacttaaagctaagat-tgaaggtacgtgcagGAGGAGGATATCAAAATGTGCTCGTGGTGGGTGCTGACGCTCTCTCAAGATACGTGGATTGGACGGACAGAGGGACGTGTATTCTATTTGGCGATGCCTC

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|71429948|gb|DR810998.1|DR810998

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAA
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGG-TTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAA

EST: gi|71429949|gb|DR810999.1|DR810999

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAGAG                         GCGGAGGTTTTCAGAATGTCTTAGTAAGTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|76291106|gb|DV030674.1|DV030674

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|149095842|gb|EE181493.2|EE181493

EST:     TTGTAGTGNGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|148935022|gb|EC879064.2|EC879064

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAG                         GCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAAT

EST: gi|101397488|gb|EB820667.1|EB820667

EST:     TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCCCTTTATCAAAG                         GCGGAAGGTTT
genomic: TTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGA-GGTTT

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), 47 (downstream exon)
Score: 165

CTGTCCGAAGTGGGGTGCACAAAAGCTTTTGGATTTGATATTACAGCTGCTTGTAGTGGGTTTTTAGTCGGCTTAATCACAGCTACTCGCTTTATCAAAGgtaattcagt ... acttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 149

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC

              aattaat  putative branch site (score: 163)
                                            tactttt  putative PPT
            aaaattaatatgtcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcagttattaaatatttatgtggttgttggtgaatcatactctcaaaattaatatgtcacttgaataatatatgcatacttttgtagGCGGAGGTTTTCAGAATGTCTTAGTAATTGGTGCAGATGCTCTTTCAAAATACGTGGATTGGACAGACAGAGGTACATGCATTCTTTTTGGTGATGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC