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

gcacgtccttcctccctgccttccctccgcgctgtctcgctcgagccgagagcattatttacgcgccgcggttttcttcgttgggctacccgccgctgaccgcccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC

Basic information

species	Zea mays
transcript	GRMZM5G826838_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G826838_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g51080.1 (Oryza sativa), 3'ss of exon 1

gcacgtccttcctccctgccttccctccgcgctgtctcgctcgagccgagagcattatttacgcgccgcggtt---ttcttcgttgggctacccgccgctga--ccgcccg---cccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC
                           | |||   |||||    | |  ||||   |||  |||    || ||   |  ||  |||||           ||   |||  ||   |  |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| 
--------------------------gcacgcacgctcgcctctgtctcgagcgccattggcgccgatcgattcggtgattgattgggagttttaattttggatccgggcggggcttgcagGTTCCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGCAACCCGCGGCTGAACCTCGCGTCG

upper sequence: GRMZM5G826838_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S68_116V6.1 (Physcomitrella patens), 3'ss of exon 1

gcacgtccttcctccctgccttccctccgcgctgtc--tcgctcgagccgagagcattatttacgcgccgcggttttcttcgttgggctacccgccgctgaccgcccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC
     |           || | |  | |  ||| |   ||| | | | | |     ||   |||     |||||        ||| |||| |   | |||  |         ||||| |   || || |||| | | |  |||||||| || |||||||||||||||| ||||||||| ||| |||| || ||||| ||  ||||  ||||||||
-----tggagaggagaggcttacattgcaagcttttgttcgtttggggcta---tgttggatacatttggcggt-------attgtgctaactatcactgttcttttcaatccagGTTCACCATTCCCGAGCGGGCAACACCCAAGGATGCCGCGTACCAGATCATCAGCGACGAGCTCATGTTGGATGGCAACCCTCGCTTGAATTTGGCGTCC

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|71298127|gb|DR785040.1|DR785040

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|148968146|gb|EE019432.2|EE019432

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|148930328|gb|EE284735.2|EE284735

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|148943210|gb|EC888270.2|EC888270

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|148939265|gb|EC883753.2|EC883753

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|74245767|gb|DT653681.1|DT653681

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|211532213|gb|FL010218.1|FL010218

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|50338197|gb|CO533323.1|CO533323

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

EST: gi|78120426|gb|DV538810.1|DV538810

EST:     TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAG                         GTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT
genomic: TCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCAT

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: 47 (upstream exon), 46 (downstream exon)
Score: 102

GAGAGATCGACGAGATGGTGCTGTCACACGGCGTCGGTGGCTCCGATGAGTCCGTCCACTCGACGTTCGCGTCCCGCTACGTCCGCACCTCCCTTCCTAGgcacgtcctt ... ccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC

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

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 111

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttacgcgccgcggttttcttcgttgggctacccgccgctgaccgcccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC

                                   cgctgac  putative branch site (score: 111)
                                            cccgccc  putative PPT
             ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacgtccttcctccctgccttccctccgcgctgtctcgctcgagccgagagcattatttacgcgccgcggttttcttcgttgggctacccgccgctgaccgcccgcccgcagGTACCGGATGCCGGAGCAGTCGATCCCCAAGGAGGCGGCGTACCAGATCATCAACGACGAGCTGATGCTGGACGGGAACCCGCGGCTGAACCTGGCGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA