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

...tttaaactagaaccatcttaatgatagactttgcgtttgtcgtctctgtacataaaattgacacgtctcccatctgtcgaccactgaacttgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCAAGACTGTTCAGCGAGAACAAGCGGGAGTACAACCGCAAAGTCCGCGAGA

Basic information

species	Zea mays
transcript	GRMZM2G022206_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G022206_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 3'ss of exon 4

tttaaactagaaccatctt-aatgatagactttgc-gtttgtcgtctctgta-cataaaattga--cacgtctcccatctgtcgaccactga---acttgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCAAGACTGTTCAGCGAGAACAAGCGGGAGTACAACCGCAAAGTCCGCGAGA
        |  ||||| |  |||| | |  |  ||    |  | |   |||| |||   ||||   ||  |     |   |  ||    |||   | |||||||||||||  ||||||||||||||||||| ||||| || |||||||||||||| || |||||||| || ||||||||||| |||||||||||||| || || ||||
--------accaccatttccaatggttgtataggctacgtagcatgcatgtagcatggtattgtatcaaatacttgaatcgctgaattgtgatgcatttgctttgcagTCTTTGCTGTGTGATCCAAACCCCAACTCTCCAGCAAACTCAGAAGCTGCCAGACTGTTTAGTGAGAACAAGCGAGAGTACAACCGCAAGGTTCGTGAGA

upper sequence: GRMZM2G022206_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ17802 (Selaginella moellendorffii), 3'ss of exon 4

tttaaactagaaccatcttaatgatagactttgcgtttgtcgtctctgtacataaaattgacacgtctcccatctgtcgaccactgaacttgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCAAGACTGTTCAGCGAGAACAAGCGGGAGTACAACCGCAAAGTCCGCGAGA
                      | | |  |||   ||| ||| || |||   |  ||| |||   |||  ||  | || | |              |||||| ||||| |||||||| ||||| ||||| || |||||||| ||||| ||| |  |||  |||||||||   || ||||||||||| | ||||||||| |
----------------------gtttggttttt--tttctcgcctttgt---tggaatagac-tttcttacacttatccatc--------------gcagTCACTGCTTTGTGATCCTAACCCAAACTCGCCGGCAAACTCCGAAGCAGCACGGATGTATAGCGAGAACCGTCGAGAGTACAACCGGAGAGTCCGCGACA

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|14245319|gb|BG873901.1|BG873901

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|113778029|gb|DW895150.1|DW895150

EST:     CAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: CAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|116820281|gb|EC863492.1|EC863492

EST:     A-CA-TGGAGTCCTATATATGATGTTG-TGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|60394682|gb|DN227552.1|DN227552

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|166554742|gb|EG174108.1|EG174108

EST:     CCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: CCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|166495293|gb|EG161210.1|EG161210

EST:     CTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: CTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|9953749|gb|BE640332.1|BE640332

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|60355643|gb|DN222616.1|DN222616

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|193502116|gb|AM937927.1|AM937927

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|14244254|gb|BG842201.2|BG842201

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTCACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|18170360|gb|BM340200.1|BM340200

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|166703203|gb|EG316942.1|EG316942

EST:     TCTTGACTTCTATTCAG                         TCCCTGTTGTGTGATCCAAACCCGAACTCCCCTGCAAAACTCAGAAGCCGC
genomic: TCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGC-AAACTCAGAAGCCGC

EST: gi|166594291|gb|EG196233.1|EG196233

EST:     TTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: TTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|31250386|gb|CD219410.1|CD219410

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|33092508|gb|CF052502.1|CF052502

EST:     GTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: GTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|213192747|gb|FM193959.1|FM193959

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTG-CTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|60348082|gb|DN215055.1|DN215055

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|211493066|gb|FL480139.1|FL480139

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|9954028|gb|BE640611.1|BE640611

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|166603394|gb|EG306821.1|EG306821

EST:     GTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: GTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|166480024|gb|EG102083.1|EG102083

EST:     GTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGC
genomic: GTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGC

EST: gi|74245427|gb|DT653341.1|DT653341

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

EST: gi|6466737|gb|AW191397.1|AW191397

EST:     ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAG                         TCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA
genomic: ACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCA

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: 1172

TATATGCTGATGGAAGCATCTGCTTGGATATCCTACAGAACCAGTGGAGTCCTATATATGATGTTGCTGCAATCTTGACTTCTATTCAGgtaccttgca ... tgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCAAGACTGTTCAGCGAGAACAAGCGGGAGTACAACCGCAAAGTCCGCGAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2017

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1981

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1174

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgtacataaaattgacacgtctcccatctgtcgaccactgaacttgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCAAGACTGTTCAGCGAGAACAAGCGGGAGTACAACCGCAAAGTCCGCGAGA

          aattgac  putative branch site (score: 1174)
                                           cttgcttt  putative PPT
      ataaaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaaactagaaccatcttaatgatagactttgcgtttgtcgtctctgtacataaaattgacacgtctcccatctgtcgaccactgaacttgctttgcagTCCCTGCTGTGTGATCCAAACCCGAACTCCCCTGCAAACTCAGAAGCCGCAAGACTGTTCAGCGAGAACAAGCGGGAGTACAACCGCAAAGTCCGCGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - -ctgtaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgaccac