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

gtaagcatgtttcttaacctgtttctctgtctttgttctatttcatccttctgttgtatcaccattacatgctttcatctgtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGACTTAAGCCCAAGCCGAAGACGGCTTAAATAGGGATTGTATTTTCCATCTC

Basic information

species	Zea mays
transcript	GRMZM2G174107_T01
intron #	8
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 8

gtaagcatgtttcttaacctgtttctctgtctttgttctatttcatccttctgttgtatcaccattacatgctttcatctgtgtgta-tagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGACTTAAGCCCAAGCCGAAGACGGCTTAAATAGGGATTGTATTTTCCATCTC
|||||   |    || | ||   ||||| | | ||  | |||   | ||||  ||| | | |       |  | | |  |   | |  |||| ||||| || ||||||||||||||||||||||||||||| || ||| |||| ||||||||||| ||| | || ||| |   |  || | || |||||| 
gtaagtccgccatttcatcttgatctctatttctgacccattgatttcttccattgaagctcacacgttttgtatgacttccctctggtagGCACTGCCATCGCACTTGCCGGAGTTTTCCTGTACTCACAACTGAAGAGACTGAAGCCCAAGCCCAAGGCTGCGTAACTGAAGCATGCAGTTGCCATCTT

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|60351427|gb|DN218400.1|DN218400

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|16378321|gb|BI992391.1|BI992391

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|211376283|gb|FL144045.1|FL144045

EST:     CATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: CATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|16377738|gb|BI992093.1|BI992093

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|13177801|gb|BG349164.1|BG349164

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|13178610|gb|BG349868.1|BG349868

EST:     AACAACAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|13150806|gb|BG321128.1|BG321128

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|148937400|gb|EC881580.2|EC881580

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|5688709|gb|AI941724.1|AI941724

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|211517932|gb|FL479804.1|FL479804

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|7227535|gb|AW566176.1|AW566176

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|13382072|gb|BG458747.1|BG458747

EST:     CTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: CTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|148940598|gb|EC885404.2|EC885404

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|83279370|gb|DV943378.1|DV943378

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|15427333|gb|BI543155.1|BI543155

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|7162621|gb|AW520243.1|AW520243

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTC

EST: gi|211376284|gb|FL144046.1|FL144046

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|13126160|gb|BG316730.1|BG316730

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

EST: gi|4624425|gb|AI615258.1|AI615258

EST:     AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCG                         GTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC
genomic: AACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGAC

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), 47 (downstream exon)
Score: 19

CCTGTCACTCATTCTGTGGGCAACTGTGTTAAACGTGTTGTGGTCATTGTAACATCAGTGCTGTTCTTCAGGACACCTGTTTCTCCTATCAACTCTCTCGgtaagcatgt ... gtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGACTTAAGCCCAAGCCGAAGACGGCTTAAATAGGGATTGTATTTTCCATCTC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 8

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 153

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttctatttcatccttctgttgtatcaccattacatgctttcatctgtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGACTTAAGCCCAAGCCGAAGACGGCTTAAATAGGGATTGTATTTTCCATCTC

                            attacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatgtttcttaacctgtttctctgtctttgttctatttcatccttctgttgtatcaccattacatgctttcatctgtgtgtatagGTACTGCGATTGCACTTGCCGGAGTTTTCCTGTACTCACAGCTCAAGCGACTTAAGCCCAAGCCGAAGACGGCTTAAATAGGGATTGTATTTTCCATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA