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

gttagttaatcctctgactggtctagctgctatttagttgcatccaacatcctaacatgcttctgttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA

Basic information

species	Zea mays
transcript	GRMZM2G144730_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 3'ss of exon 4

gttagttaatc---ctctgactggtctagctgctatttagttgcatccaacatcctaacatgcttctgttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA
||  ||| ||    |  | ||  ||  | |  |||  |||||     ||| || || |||| |||||| |  ||||||||| |||||||| |||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||||||||| |||||||| |||||| | |||||
gtcggttgatttctccataacatgttcaacctctagatagttatgcacaagatgctgacatccttctgctttaacagAGAAAGATTGGGAGGACATAAAGTTTGGTGTTGAAAATGGTGTTGATTTCTATGCCGTTTCCTTTGTGAAGGATGCAAAAGTTATTCATGAACTGAAGGA

upper sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 3'ss of exon 4

-----------------gttagttaatcctctgactggtctagctg--ctatttagttgcatccaac--atcctaacatgcttctg-ttcca-acagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA
                  ||    |||    ||  |     ||||   ||| | |  ||  |   |    |  ||   || || |   ||||  |||| || ||||||||||||||||||||||| || || |||   || |||||||| || || |||||||| |||||||| |||||| ||||||| || ||| |
gttgataccagctgatgtttttccaatatcttgcatcaaggagcttttctaataaaatgtttttgagtggttatattctggttttaactccacgcagACAAAGATTGGGAAGACATAAAATTTGGAGTGGACAACCAAGTCGATTTCTACGCCGTCTCCTTTGTTAAGGATGCTAAAGTTGTCCATGAGTTGAAGAA

upper sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 4

----------------------------------------------------------------------------------gttagttaatcctctgactggtctagctgctatttagttgcatccaacatcctaacatgcttc----tgttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA
                                                                                   ||  ||  ||  || ||  ||        |  | |     ||||||  |  |  |||   ||      || ||||||| || || |||||||| || || ||||| || || |||   |||||||||||||| |||||||||||||| |||||  ||||  ||||||| || || ||
gttatcttttgttcttatgttttttctaataggtgattttctgtttctattttccacgaagttgatatgatgtttcttttacttttatttgtctacttacgtgttatttgaattgtaaaaaatatccaatcttttcccattactcatgtcatttcaacagACAAAGACTGGGAAGATATCAAGTTTGGAGTGGACAACCAAGTTGATTTCTATGCTGTTTCCTTTGTGAAAGATGCTGAAGTGGTCCATGAGTTGAAAGA

upper sequence: GRMZM2G144730_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3

-----------------gttagttaatcctctgactggtctagctgctatttagttgc--atccaacatcctaacatgcttctgttc-------caacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA
                  | | |   ||    ||    |  |  |  ||| |     |  |      || | |   || |||  |         |  |||||||||||||||||||||| |||||||| || |||||    ||||||||||| ||  | || ||||| ||||| ||| | ||  | |||||  | ||   
aatttcattagtgtgcaatcactatctctagagatctatagaaattttatctgaacacggactttggataccattgtgtttccttctgtggagtctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATC

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|32930333|gb|CF035145.1|CF035145

EST:     AAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT
genomic: AAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

EST: gi|71764041|gb|DR961978.1|DR961978

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

EST: gi|148966755|gb|EE017835.2|EE017835

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATT

EST: gi|26456209|gb|CA827792.1|CA827792

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAATGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

EST: gi|32935309|gb|CF040121.1|CF040121

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

EST: gi|149048881|gb|EE048381.2|EE048381

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGAGAAGACATAAAATTTGGTGT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGT

EST: gi|78075400|gb|DV503834.1|DV503834

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

EST: gi|20301238|gb|BQ164181.1|BQ164181

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAATGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

EST: gi|148958744|gb|EC905021.2|EC905021

EST:     GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTG                         AGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT
genomic: GCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 243

GCTGATACAGTCAAGTGTGAAGTAGTTGACGGCGGGGAATTGAAATCAAGGCGCCACCTAAATGTTCGTGGAAAAAGTGCTACTTTGCCATCTATCACTGgttagttaat ... gttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 319

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ggtctagctgctatttagttgcatccaacatcctaacatgcttctgttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA

                              tcctaac  putative branch site (score: 319)
                                        cttctgttcc  putative PPT
           tatttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttaatcctctgactggtctagctgctatttagttgcatccaacatcctaacatgcttctgttccaacagAGAAGGATTGGGAAGACATAAAATTTGGTGTCGAAAACGGTGTTGATTTCTATGCAGTTTCCTTTGTGAAGGATGCCAAAGTTATCCATGAATTAAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG