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

gtgctgaatgacatggtaattattgtgttaaatcaggtttagcatggaaacataacttttctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA

Basic information

species	Zea mays
transcript	GRMZM2G124886_T04
intron #	17
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 17

gtgctgaatgacatggtaattattgtgtt----aaatcaggt-ttagcatggaaacataacttttctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA
||||    ||   || ||||||||||  |    || |||||  | || ||   || |||||  || | ||||||||||||||||||||||||||||||| || |||||||| |||||||| ||||||||||| ||| ||||||||||||||||| |||| |||||||||||||| 
gtgccccctgttctgctaattattgtactctgcaactcaggcctcagaatctgaagataacccttttatttgcagTGTGGCACGTTTCTTGGAATCACGGGGCATGTTGGAAGAAGCCCTTGAGATAGCAACAGACTCTAATTACAGATTTGACTTGGCCGTGCAGCTTGGTCGG

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 8

gtgctgaatgacatggtaattattgtgtt----aaatcaggt-ttagcatggaaacataacttttctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA
||||    ||   || ||||||||||  |    || |||||  | || ||   || |||||  || | ||| ||||||||||||||||||||||||||  || |||||||| |||||||| ||||||||||| ||| ||||||||||||||||| |||| |||||||||||||| 
gtgccccctgttctgctaattattgtactctgcaactcaggcctcagaatctgaagataacccttttattttcagTGTGGCACGTTTCTTGGAATCACAGGGCATGTTGGAAGAAGCCCTTGAGATAGCAACAGACTCTAATTACAGATTTGACTTGGCCGTGCAGCTTGGTCGG

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17

---------------------gtgctgaatgacatggtaattattgtgt--taaatcaggttta--gcatggaaacataa----cttttctctttgc-agTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA
                         ||||  | |    ||||||| ||   |   | | ||||   |||||  || |  |     | ||    |||| |||||||| ||||||||||||||||| || ||| | ||||| ||||| ||  |||| |||||| || ||||| ||||||| || ||  ||||||||||  ||
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA

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|33093602|gb|CF053596.1|CF053596

EST:     ATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCACGTTTCTTGGAATCACGTGGAATG-TGGAGGAAGCCCTCGAGAT
genomic: ATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctgaatg ... ctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGAT

EST: gi|111145650|gb|EE257974.1|EE257974

EST:     GGAACAATATGACAG                         TGTGGCACGTTTCTTGGAATCACGTGGAATGTTGAAGGAAGCCCTCGAGAT
genomic: GGAACAATATGACAGgtgctgaatg ... ctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGAT

EST: gi|32929286|gb|CF034098.1|CF034098

EST:     GATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctgaatg ... ctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGAT

EST: gi|60337834|gb|DN204807.1|DN204807

EST:     GATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAG                         TGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGAT
genomic: GATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctgaatg ... ctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 343

TACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCAAAGGAACAATATGACAGgtgctgaatg ... ctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 438

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 463

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 562

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtaattattgtgttaaatcaggtttagcatggaaacataacttttctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA

                                  acataac  putative branch site (score: 562)
                                        cttttctctttgc  CT-rich tract
                                    ataactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgaatgacatggtaattattgtgttaaatcaggtttagcatggaaacataacttttctctttgcagTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT