ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTCAGTAGGTCCTCGCATGCCCATGTTTCCACCTGGTGTCCCTGGAGTTGGTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctcattttatgatgtacatgtacacccactgttccaaattatacaacattttgggttttatagatcataatttttgcacttaaatatattatg...

Basic information

species	Zea mays
transcript	GRMZM2G102829_T04
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G102829_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g02700.1 (Oryza sativa), 5'ss of exon 6

TTCAGTAGGTCCTCGCATGCCCATGTTTCCACCTGGTGTCCCTGGAGTTGGTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatg----ctcattttatgatgtacatgtacacccactgt-tccaaattatacaacattttgggttttatagatcataatttttgcacttaaatatattatg
|||||| |||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| || ||||| || |||||| | |||||| ||      | ||||| | ||  |  ||| |        | | |   ||  | || | |     |||| |      |    | ||   |    |  |  || 
TTCAGTTGGTCCTCGCATGCCCATGTTTCCACCTGGTGTTCCTGGAGTTGGACAGCAACTGTTCTATGGTCAGCCCCCTCCAGCGTTTATCAACACACAGgtaaataaggcttaattttcttattgatgtgttcttttgacatcttctctttccataataatcccccttttttttggtgt----tgtgtgttagtgtgcacaat-

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|37399906|gb|CF637295.1|CF637295

EST:     TTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCTTTCATCAACCTTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|211302758|gb|FL258854.1|FL258854

EST:     GTCAGCAKCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|60359019|gb|DN225992.1|DN225992

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|37396074|gb|CF635324.1|CF635324

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCTTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|6526993|gb|AW216219.1|AW216219

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|40337375|gb|CK371445.1|CK371445

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|67014795|gb|CO443544.1|CO443544

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|5268845|gb|AI770809.1|AI770809

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|211302756|gb|FL258852.1|FL258852

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

EST: gi|33092472|gb|CF052466.1|CF052466

EST:     GTCAGCAGCTGTTCTATGGTCAGCCACCACCTTTTTTCATCAACCCTCAG                         GCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT
genomic: GTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGT

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: 575

TTCAGTAGGTCCTCGCATGCCCATGTTTCCACCTGGTGTCCCTGGAGTTGGTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctc ... tgtttcttagGCTGGATTTGCTTTCCAGCAACCTCTGATGCCTGGTATGAGGCCTGGTGGTCCAATGCCGAACTTTATGATGCCTATGGTTCAGCAAGGACAGCAACCAC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 631

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 539

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 355

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGTAGGTCCTCGCATGCCCATGTTTCCACCTGGTGTCCCTGGAGTTGGTCAGCAGCTGTTCTATGGTCAGCCACCACCAGCCTTCATCAACCCTCAGgtacatgctcattttatgatgtacatgtacacccactgttccaaattatacaacattttgggttttatagatcataatttttgcacttaaatatattatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT