ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaaccgatccccctttccacagccgtagtccaattctgcgcggctaaactcgatcggaggatcgtgtttcgattgggtttatggtttgttttgat...

Basic information

species	Zea mays
transcript	GRMZM2G147046_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G147046_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g53310.1 (Oryza sativa), 5'ss of exon 1

CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtac--acaaccgatccccctttccacagccgtagtccaattctgcgcggctaaactcgatcggaggatcgtgtttcgattgggtttatggtttgttttgat
||||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| |   |  ||||||| |||   |   |  ||  |     | | ||  || |   || ||     ||| |  ||  |  |  |||| |   |  | | |  
CGAGTTCGTGCCCTACGAGGGGGACACCGTGTCGGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCCGGCATCGACCTCACGgtgcccgcccccgatcctcctcgtcttcgttgtgcttttgattttcgatgcaaggatctataactagatgggtttatgggtttgttttttcgtgatctgg--

upper sequence: GRMZM2G147046_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA20G28900.1 (Glycine max), 5'ss of exon 1

CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgt--acacaaccgatccccctttccacagccgtagtccaattctgcgcggctaaactcgatcggaggatcgtgtttcgattgggt--ttatggtttgttttgat--
||||| ||| |  || |||||||||||||| || |||||||| || ||||||||||| ||||| ||||||||||| || ||||| || || ||  |||||||     ||| |  |  | |||| | || |  || ||  |||   |      |  || | |    |  ||   | || |||   |  | | ||||| ||||  |  
CGAGTACGTACTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGACATTTTCTGGAGCTCTGATCACCCCGGCATTGATTTCACGgtcagtgcaatctctatcacttttctcatc--taatc--atttgccctaatca--cttgctaattgactcaattatcaatttactggtgagggtttatttttttag

upper sequence: GRMZM2G147046_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G38880.1 (Glycine max), 5'ss of exon 1

CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgt--acacaaccgatccccctttccacagccgtagtccaattctgcgcggctaa-actcgatcggaggatcgtgtttcgattgggtttatggtttgttttgat
||||| |||||  || |||||||||||||| || |||||||| || ||||||||||| || || ||||||| |||||| ||||| || || ||  |||||||     ||| |  |  | |||| | || |            ||   |   |   | | ||    |  |||   || |  | ||||||  | ||| |||||  
CGAGTACGTGCTTTACGAGGGCGACACCGTTTCGGGGAACTTTGTTGTCGTCGACCATGATATTTTCTGGAACTCCGATCACCCCGGCATTGATTTCACGgtcagtgcaatctctatcacttttctcatctaatcatttgccctaatcacttgctaattgactcaattatcaatttactttggggttttcgattt-ttttg--

upper sequence: GRMZM2G147046_T01 (Zea mays), 5'ss of exon 1
lower sequence: AT3G22845.1 (Arabidopsis thaliana), 5'ss of exon 1

CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaacc----gatccccctttccacagccgtagtcc--aattctgcgcggctaaactcgatcggaggatcgtgtttcgattgggtttatggtttgttttgat
 |||| ||| |  || || |||||||| || ||||| ||||||||||||||||| || || ||||||||| | ||||| || || ||  | ||  |||||||   | | |     ||   |||||  ||  |   ||| |  || | ||    | |    |||||   |    |    || ||||     |    || || ||   
AGAGTACGTCCTTTACGAAGGCGACACTGTTTCCGGTAACTTCGTCGTCGTCGATCATGATATCTTCTGGGGATCCGATCATCCTGGTTTGGATTTCACGgttagcgatctttcaatttacctttttaccccaaaagttcttaactttgatacgtttccttcgat---aatcccaatgtttgatttatcgtgaaattggtgtt---

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|60350490|gb|DN217463.1|DN217463

EST:     CTCCGACCACCCAGGAATCGACCTCACG                         GTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT
genomic: CTCCGACCACCCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT

EST: gi|161591972|gb|EY961607.1|EY961607

EST:     TCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACG                         GTAACGTCACCAGGTGGCAACACTGTGTACACATTG
genomic: TCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTG

EST: gi|60339915|gb|DN206888.1|DN206888

EST:     CACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACG                         GTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT
genomic: CACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT

EST: gi|32859851|gb|CD999532.1|CD999532

EST:     TCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACG                         GTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT
genomic: TCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT

EST: gi|71763107|gb|DR961044.1|DR961044

EST:     CCAGGAATCGACCTCACG                         GTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT
genomic: CCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT

EST: gi|60353926|gb|DN220899.1|DN220899

EST:     GAATCGACCTCACG                         GTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT
genomic: GAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT

EST: gi|56461951|gb|CK986249.1|CK986249

EST:     TCGACCACGACATCTTCTGGAGCTCCGATCACCCAGGCATCGACCTCACG                         GTAACGTCACCAGGTGGTAACACTGTGCACACATTGAAGGGAAAATCTGGT
genomic: TCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGT

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: 173

CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaacc ... gtaaatacagGTAACGTCACCAGGTGGCAACACTGTGTACACATTGAAGGGAAAATCTGGTGAGAAATTTGAGTTTAAAGCTCCAAGAGGTGGCATGTATAAGTTCTGCT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 370

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGTTCGTGCCCTATGAGGGCGACACCGTGTCCGGGAACTTCGTCGTCGTCGACCACGACATCTTCTGGAGCTCCGACCACCCAGGAATCGACCTCACGgtacacaaccgatccccctttccacagccgtagtccaattctgcgcggctaaactcgatcggaggatcgtgtttcgattgggtttatggtttgttttgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT