ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcctccctctccctcttcctctcctccctagcaatctggcacgtttgttttcctttataggatgttgtgttctagccatctcacttcagctcaa...

Basic information

species	Zea mays
transcript	GRMZM2G053767_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G053767_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g56670.2 (Oryza sativa), 5'ss of exon 4

GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcctccctctccctcttcctctcctccctagcaatctg-gcacgtttgttttcctttataggatgttgtgttctagccatctcacttcagctcaa-
||| || |||||||||||| |||||||| ||||| ||||||  ||||| ||||||||||||||| |||| |||||||| ||| ||| ||||| ||||  ||||||           ||| | |    | |||| |  | |||       |||| ||  ||||||| |||| |     
GTACAACATGGGTGTAATTCCAACAAAAAAGAGCCTGTTAACATGTGAAAAACTTTCAGTGAGCTCCTTTTGCAGgtc-ctttctctctctctctctctctctccatgtatatgtgctgtgtagccatcttttaccatttagtggcaaatgtt-tactcatctcagttcaacaattg

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|166571459|gb|EG188984.1|EG188984

EST:     AGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|60342340|gb|DN209313.1|DN209313

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|50324650|gb|CO519776.1|CO519776

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTTTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCCCCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|211018457|gb|FL453049.1|FL453049

EST:     AAARAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTYTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|50324261|gb|CO519387.1|CO519387

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|60395364|gb|DN228233.1|DN228233

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|71438629|gb|DR819679.1|DR819679

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|211245445|gb|FK950833.1|FK950833

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|211430616|gb|FL465154.1|FL465154

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|31664102|gb|CD573282.1|CD573282

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|211245444|gb|FK950832.1|FK950832

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACWTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|211526429|gb|FL471796.1|FL471796

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|78122122|gb|DV540506.1|DV540506

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|60343595|gb|DN210568.1|DN210568

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|6431873|gb|AW172077.1|AW172077

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|78122121|gb|DV540505.1|DV540505

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|6342793|gb|AW165617.1|AW165617

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGCCTTGCACCAGTTATGGTGAAGCTCAAGTTTGCAGAGCCCCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|33103763|gb|CF063723.1|CF063723

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|32945068|gb|CF049887.1|CF049887

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|71759525|gb|DR957462.1|DR957462

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|213172151|gb|FM193873.1|FM193873

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAGCTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

EST: gi|50325006|gb|CO520132.1|CO520132

EST:     AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAG                         GCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA
genomic: AAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAA

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), 49 (downstream exon)
Score: 73

GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcct ... attcttgcagGCGGAGACTTGCAACAGTTATGGTGAAGCTCAAGTTTGCAGAGCACCTTAAGGAGGCTGTGACGTACATCGAACAGGGGCACGTGCGTGTCGGTCCAGAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 50

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 32

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATAATATGGGTGTAATTTCAACAAAAGAGAGCTTGTTAAAGTGTGAGAAACTTTCAGTGAGCGCCTTCTGCAGgtctcttcctccctctccctcttcctctcctccctagcaatctggcacgtttgttttcctttataggatgttgtgttctagccatctcacttcagctcaa

- - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG