ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctccatttttatttatttgacgctcaatagttcagatttgcactaacaaacgtcaaataaaaaaaaatcggagggagtattagctaaatgata...

Basic information

species	Zea mays
transcript	GRMZM2G180863_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G180863_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g41360.1 (Oryza sativa), 5'ss of exon 3

CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctccatttttatttatttgacgct-caatagttcagatttgcac-taacaaacgtcaaataaaaaaaaatcggagggagtattagctaaatgata
 |||||||| ||  ||||||| || ||||| |||||||| || ||  |||||||||| ||||| |||||||||||||| ||||||||||| |||||||||||| |   |  | | ||| ||  | |  | | |  ||   ||  | ||    ||   | | |||   ||    |  |     |||    |   |   | || 
TATGGAGCTTTTTGTCATGATCGACGCATGTCGGCGGGCGTCGGCGAGGTCTATTACTGTTGTCATTCCATACTTTGGGTATGCCAGAGCTGACAGAAAGgta-tgtataaactcttaattgatggctgttgcggtatgccaagtgtgtttgtactgatcatcatgcaatttcatttttactggatatcttcttcccttat-

upper sequence: GRMZM2G180863_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S212_43V6.1 (Physcomitrella patens), 5'ss of exon 2

CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctccatttttat----ttatttgacgctcaatagttcagatttgcactaacaaacgtcaaataaaaaaaaatcggagggagtattagctaaat-gata------------------------------------
 |||||||| ||  |||||||||| ||||||||||| || ||||||  | | ||||||| ||| || ||||||||||| || ||||| |||||  | |||||   |   |   ||  ||    ||  |||   ||||    |  |   |   || | |    |  | |||      | ||  | || | || | | |||  ||||                                    
TATGGAGCTTTTGGTCATGATTGACGCATGCCGGCGAGCATCAGCAAAGACCATTACCGCTGTGATCCCATACTTTGGGTACGCCAGGGCAGATCGTAAGgtgagaagactggttaaatgaattttcttgcgactcagctctagaagatgttaccagc--ttggaacatatttgtcagtcaaatggtg-atcatcgaaacagatatttctgctgtgtttaaatttggcagtgttttgacag

upper sequence: GRMZM2G180863_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S152_123V6.1 (Physcomitrella patens), 5'ss of exon 3

CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgt--actagctccattttta---tttatttgacgc------tcaatagttcagatttgcactaacaaacgtcaaataaaa--aaaaatcggagggagtattagctaaatgata----------------------------------
 |||||||| || || ||||||||||||||||| || || ||||||    |||| |||| ||| || ||||||||||||||||| ||||| ||  | |||||       |   ||   ||   ||||| | ||||      | ||   ||  | |  ||   ||         | | | |    || ||   |  | || |  |  | |  |                                   
GATGGAGCTTTTAATTATGATTGATGCATGCCGACGAGCATCAGCAAAAACTATCACCGCTGTCATACCATACTTTGGTTATGCTAGAGCTGATCGGAAGgttaggagacctgatcgataggttttatgttacgcattttgtaaacgttttggctgggccggaatgtctccttagtcagattgcaagtcattgatactaatctccgattattgtgctgatatacatgctttgaacttgttttgatag

upper sequence: GRMZM2G180863_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ12994 (Selaginella moellendorffii), 5'ss of exon 2

CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctccatttttatttatttgacgctcaatagttcagatttgcactaacaaacgtcaaataaaaaaaaatcggagggagtattagctaaatgata
 ||||||||  |  ||||||| || ||||||||||| || || ||   | | || || |  || |||||||||||||| || |||||||| |||||||||||| |  ||    |     || ||   |  |||||     | |  |    | |      |||                                      
GATGGAGCTACTGGTCATGATAGACGCATGCCGGCGTGCATCCGCCAAGACCATCACAGCAGTAATTCCATACTTTGGATACGCCAGAGCTGACAGAAAGgtagtcactgtgatccagcttttt---ctttcaat---ctacacgtcgtgtgatgtttttcag-------------------------------------

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|149088668|gb|EE177786.2|EE177786

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|78088529|gb|DV516922.1|DV516922

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|149112871|gb|EE191452.2|EE191452

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|6626351|gb|AW257883.1|AW257883

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCGAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|74240297|gb|DT648211.1|DT648211

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|149006976|gb|EE040195.2|EE040195

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|50325135|gb|CO520261.1|CO520261

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCT

EST: gi|71770134|gb|DR968071.1|DR968071

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|31354391|gb|CD438748.1|CD438748

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|149000114|gb|EE037239.2|EE037239

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|71766416|gb|DR964353.1|DR964353

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|149079724|gb|EE168725.2|EE168725

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|148973790|gb|EE024926.2|EE024926

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

EST: gi|148947744|gb|EC893227.2|EC893227

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTNCA-GGGCGTGAACCCATTACTGCCAAAC
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCT-CAAGGGCGTGAACCCATTACTGCCAAAC

EST: gi|91874828|gb|EB404785.1|EB404785

EST:     CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAG                         GCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT
genomic: CTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACT

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: 88

CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctc ... ggtaactcagGCTCAAGGGCGTGAACCCATTACTGCCAAACTTGCTGCAAATTTACTTACTGAAGCTGGTAGTGACCGTGTCATTGTATGTGATATTCATTCTACGCAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 67

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 81

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGAGCTCTTCATCATGATTGATGCATGCCGGCGGGCTTCAGCACGGTCTATTACCGTTGTTATTCCATACTTTGGTTATGCCAGAGCAGACAGAAAGgtactagctccatttttatttatttgacgctcaatagttcagatttgcactaacaaacgtcaaataaaaaaaaatcggagggagtattagctaaatgata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG