ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTCCTGGGATGAAGCAGCGTCCACCACGTGGGTATAATCCATACCATGGCTACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtctttgtggtgcactattacaatgtggatttctagttttcttttctaacataaccttttgcggttttgcag

Basic information

species	Zea mays
transcript	GRMZM5G862331_T04
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G862331_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 5'ss of exon 5

TTCCTGGGATGAAGCAGCGTCCACCACGTGGGTATAATCCATACCATGGCTACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtct---ttgtggtgcactattacaatgtggatttctagttttcttttctaacata-accttttgcggttttg--cag
| ||||||||||||||||||||||| ||||| || ||||| || ||||| ||||| |||||||| || ||||| || |||||||| ||||||||||| |||||||| |   || |    ||  ||     | |   | | ||  | |  | ||||||||  |  || ||   | |||  |||
TCCCTGGGATGAAGCAGCGTCCACCGCGTGGATACAATCCTTATCATGGTTACCCATATAGATCGTATGGGGCCCCATATTTCCCACCATATGGTTACGGgtaagtttagcttttttgacaacatggatgtctaattctttatgtctggtgtctaacatccatattgtgtattcttgttcag

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|74240412|gb|DT648326.1|DT648326

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|74244705|gb|DT652619.1|DT652619

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|71427532|gb|DR808582.1|DR808582

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTTTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|71419429|gb|DR804766.1|DR804766

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|26559376|gb|CA831611.1|CA831611

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGGCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|8367197|gb|BE050133.1|BE050133

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|113701557|gb|EE679061.1|EE679061

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGGCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|91051981|gb|EB162399.1|EB162399

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCCCCGCCCTATGCGCTACAGACCTTTCTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|71436658|gb|DR817708.1|DR817708

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAG

EST: gi|74240413|gb|DT648327.1|DT648327

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|28987157|gb|CB351492.1|CB351492

EST:     ACCCTTATAGATCATACGGGGCACCGTATTTNNNNNNNATATGGTTATGG                         GAGGGCTCCTAG
genomic: ACCCTTATAGATCATACGGGGCACCGTATTTCCCCCC-ATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAG

EST: gi|31911181|gb|CD651796.1|CD651796

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|28361626|gb|CB239982.1|CB239982

EST:     ACCCCTTATAGATC-TACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGG-CTCCTAGATT
genomic: ACCC-TTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATT

EST: gi|6721087|gb|AW308724.1|AW308724

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGGCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|101392226|gb|EB818041.1|EB818041

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCT
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCT

EST: gi|93015249|gb|EB640769.1|EB640769

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|74237334|gb|DT645248.1|DT645248

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|89759138|gb|DY688052.1|DY688052

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|9254701|gb|BE345169.1|BE345169

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGGCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|74234517|gb|DT642431.1|DT642431

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|14244084|gb|BG841816.2|BG841816

EST:     AGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: AGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|74244706|gb|DT652620.1|DT652620

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|60351779|gb|DN218752.1|DN218752

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|87156058|gb|DY400847.1|DY400847

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGGCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|71427533|gb|DR808583.1|DR808583

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|211216543|gb|FL246888.1|FL246888

EST:     CTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: CTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|22715374|gb|BU197729.1|BU197729

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGCTCCTAGATTCCGGCGCCCTATGCGCTACAGACCTTACTTCTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

EST: gi|86470105|gb|DY236475.1|DY236475

EST:     TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGG                         GAGGGTTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTATTTTTGAAG
genomic: TACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAG

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: 685

TTCCTGGGATGAAGCAGCGTCCACCACGTGGGTATAATCCATACCATGGCTACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtcttt ... ggttttgcagGAGGGCTCCTAGATTCCGCCGCCCTATGCGCTACAGACCTTACTTCTGAAGTACGGGGTAGGGTAATGAAGTTCAATGCAAAACCAGCCCATGGTCACTG

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 167

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 277

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTGGGATGAAGCAGCGTCCACCACGTGGGTATAATCCATACCATGGCTACCCTTATAGATCATACGGGGCACCGTATTTCCCCCCATATGGTTATGGgtaagtctttgtggtgcactattacaatgtggatttctagttttcttttctaacataaccttttgcggttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA