ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatgttcctttgagattccataccatccacccgttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctag

Basic information

species	Zea mays
transcript	GRMZM2G023528_T05
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G023528_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 5'ss of exon 6

GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatgttcctttgagattccataccatccacccgt-tgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctag
||||||| ||| || |||||||||||||||||||| ||  ||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||| ||     || | |  | || ||||| |||     | |     | ||||||  || ||  ||    ||  ||||       |    || |||
GAAGAAGTGTACTCGAAAGATCGGGTAATTGTTGCTGTAAGGCAAGGGAACATCCTCGCTACTGCTTTTCACCCAGAATTGACATCAGACTCTAGATGgttagtgccttttcct--acataccatatcatgttttcatgcatcttgtttag--gctctgatgctcatggatctgtctgctcctgcttgatag

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|15079808|gb|BI388841.1|BI388841

EST:     TGCTTTCCCCCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: TGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|50327771|gb|CO522897.1|CO522897

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|6020368|gb|AW065296.1|AW065296

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|71318383|gb|DR795955.1|DR795955

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|5714344|gb|AI944329.1|AI944329

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|5895630|gb|AW036876.1|AW036876

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|32934367|gb|CF039179.1|CF039179

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGAT
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGAT

EST: gi|33467208|gb|CF244257.1|CF244257

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|37382875|gb|CF628406.1|CF628406

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|74233030|gb|DT640944.1|DT640944

EST:     AACATCCTCGCAACTGCTTTCCCCCCAGAATTGACATCAGACTCCAGATG                         GCATCGNNNNNNNNNGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTT
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|91055148|gb|EB165566.1|EB165566

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTTTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTT
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|15215333|gb|BI431244.1|BI431244

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|31359368|gb|CD443725.1|CD443725

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|78021493|gb|DV489880.1|DV489880

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|5804744|gb|AI979714.1|AI979714

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTN
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|60340407|gb|DN207380.1|DN207380

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|5804728|gb|AI979698.1|AI979698

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|40303169|gb|CK347556.1|CK347556

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|5597195|gb|AI891188.1|AI891188

EST:     CCTCGC-ACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: CCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

EST: gi|18166881|gb|BM336720.1|BM336720

EST:     AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATG                         GCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC
genomic: AACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTC

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), 42 (downstream exon)
Score: 5

GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatg ... gttgtgctagGCATCGTTTCTTCTTGGACATGGATAAAGAATCCCCAGCAAAGGCGTTTTCTGCGCTCTCCCTGTCGTCATCGTCAAGAGACACTGAAGGCCTGCCAAAG

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 8

Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 12

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 8

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGAGTATTCAAAAGATCGGGTAATTGTTGCAGTGCGGCAAGGGAACATCCTCGCAACTGCTTTCCACCCAGAATTGACATCAGACTCCAGATGgtaagcaatgttcctttgagattccataccatccacccgttgggtggtttagccgccctcttgtcgctgactctgaaaagctcgttgtgctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG