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

...ttagcattttgtatgcaatttacaatatcattgtattttttttaaaccaagtcgatattgccatatagagtgacatacattctaaggcgccttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCTCAACACGATTGCAGTTTTCGTGCTGGTCGTGGCAAAATTGCCGAACATG

Basic information

species	Zea mays
transcript	GRMZM2G064898_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G064898_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g26940.3 (Oryza sativa), 3'ss of exon 1

ttagcattttgtatgcaatttacaatatcattgtattttttttaaaccaagtcgatattgccatatagagtgacat--------acattctaaggcgccttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCTCAACACGATTGCAGTTTTCGTGCTGGTCGTGGCAAAATTGCCGAACATG
     | ||  |   |    ||  ||    ||   | |      |||  ||  | | ||    | | || || |||        | || || |  | | || || |||||| || || ||||| ||||||||||||||||| ||||| ||| |||| |||||||| ||||||||| | || || || || |||||  |||| ||||||
-----agttgattctc---ctatgatgcttttaactctcaggccaacagagatgctctttttttcttgaatggcatgttctaagatatgctcatacactttgttgcagGTACCTGATCGCGTCACACTTGACCGACTACAAACAGCCAATGCTTTTCCTCAACACCATTGCAGTTCTGGTACTAGTGGTAGCAAAGCTGCCAAACATG

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|8665634|gb|BE186450.1|BE186450

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|69350983|gb|DR451981.1|DR451981

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|67021272|gb|CO450021.1|CO450021

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211356382|gb|FL426368.1|FL426368

EST:     GCAGCTTACTGGGAAACAGGAAGTTTTTAACTGGGGNACCTGGNGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAA
genomic: GCAGCTTACTCGGAA-CAGGAAGTTTTTAACTGTGGTACCTGT-GGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAA

EST: gi|211210546|gb|FL434835.1|FL434835

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|88751304|gb|DY535445.1|DY535445

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|76019193|gb|DT946363.1|DT946363

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211272281|gb|FL097588.1|FL097588

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|76916955|gb|DV166624.1|DV166624

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211506658|gb|FL391679.1|FL391679

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|8665333|gb|BE186149.1|BE186149

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211028254|gb|FL437879.1|FL437879

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|37361478|gb|CF602767.1|CF602767

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|60340594|gb|DN207567.1|DN207567

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211272286|gb|FL097593.1|FL097593

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|28983205|gb|BQ538548.2|BQ538548

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|5006053|gb|AI712115.1|AI712115

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|76916953|gb|DV166623.1|DV166623

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|89757569|gb|DY687115.1|DY687115

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTTGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|91871327|gb|EB401360.1|EB401360

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGNNNNNNNN
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|9028613|gb|BE238653.1|BE238653

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211274081|gb|FL097595.1|FL097595

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|78026678|gb|DV495065.1|DV495065

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|211274083|gb|FL097597.1|FL097597

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTGATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

EST: gi|91871328|gb|EB401361.1|EB401361

EST:     CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCT                         GTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT
genomic: CAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCT

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: 89

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGGAAGTTTTTAACTGTGGTACCTGTGGTGCTgtaagttcca ... cttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCTCAACACGATTGCAGTTTTCGTGCTGGTCGTGGCAAAATTGCCGAACATG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 139

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

accaagtcgatattgccatatagagtgacatacattctaaggcgccttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCTCAACACGATTGCAGTTTTCGTGCTGGTCGTGGCAAAATTGCCGAACATG

                                          cgccttctt  CT-rich tract
                 atataga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagcattttgtatgcaatttacaatatcattgtattttttttaaaccaagtcgatattgccatatagagtgacatacattctaaggcgccttcttacagGTATCTTATTGCGTCGCACTTGACCGACTACAAGCAGCCGATGTTTTTTCTCAACACGATTGCAGTTTTCGTGCTGGTCGTGGCAAAATTGCCGAACATG

- - - - -tgtatgc
- - - - - - - - - - - - - - - -tgtattt
- - - - - - - - - - - - - - - - - - - - - -aaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acataca