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

gtaatctgttttgtgtacccttttgatttccctaatgaattgtatttgtatttttctaatatatgttcatctgcatggttctgaataccttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG

Basic information

species	Zea mays
transcript	GRMZM2G075551_T03
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G075551_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g02500.1 (Oryza sativa), 3'ss of exon 4

-------------------------------------gtaatctgttttgtgtacccttttgatttcccta-atgaattgtatttgtattttt--ctaatatatgttcatctgcatggttctgaatacct--------tcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGT---CGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG
                                      |    | | || |||    | | | |   | || ||  |||     |  | | ||   || ||  ||||||     ||  ||||||  |  |        |     |||||||| |||||||||| ||||||||| ||||||||  | ||    || |||||||| ||||||||||| || |||||||||||||||||||||||||||    
gtaatgtgtttacttggtgcagcgaacttctcttctactgccttttcttttgtgaagtatgggtgcacatacatatattcccccttcactcttacatattaattgttcaggactatatttctgataagttcactgtggttacaacagAGGTTCAAGGAAATGAAAGAAATGCAAAGCAGCAGCAGCAGCAGCCGTGATGACAGGCAGAAACGTGAGCAGCAACGAGAAGAGAAGGAGCTGGCAAAAT---

upper sequence: GRMZM2G075551_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g00320.t01 (Vitis vinifera), 3'ss of exon 6

gtaatctgttttgtgtaccct------tttgatttccctaatgaattgtatttgtatttttctaatatatgttcatctgcatggttctgaatacct-tcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG---
|| |  || ||| | ||| ||      |||  ||   |     |||| | |||| | ||      | | | |  ||||  |   | ||   ||     | | ||||||||||||||||||||||||||||||   | | | | | ||||| |||||  | || ||||| |||||||||||  |||||  |||| |||| ||  |||   
gtgaa-tgctttttatactctgaaaaattttgttggtcaggaaaattatttttgaagttcaaggctttctctaaatctaaagtttgcttggtatgggcctttgcagAGGTTTAAGGAAATGAGAGAAATGCA---CGGTACTAGCAGTCGTGATGATCGGCAAAAACGAGAACAACAACGTCAAGAGCGGGAGATGGCTAAGTTTGCTC

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|76285589|gb|DV025157.1|DV025157

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|78121467|gb|DV539851.1|DV539851

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|71422270|gb|DR805672.1|DR805672

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|76282171|gb|DV021739.1|DV021739

EST:     TTGAGAGTCACTTGAGGTCATATGACCACATTCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: TTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|74234698|gb|DT642612.1|DT642612

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGA
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGA

EST: gi|74244524|gb|DT652438.1|DT652438

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|60358695|gb|DN225668.1|DN225668

EST:     ATCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|71324315|gb|DR798858.1|DR798858

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|71324316|gb|DR798859.1|DR798859

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|93281364|gb|EB673628.1|EB673628

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|71422269|gb|DR805671.1|DR805671

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|93281363|gb|EB673627.1|EB673627

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|71322954|gb|DR798154.1|DR798154

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|76290174|gb|DV029742.1|DV029742

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|71433465|gb|DR814515.1|DR814515

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

EST: gi|76011266|gb|DT938436.1|DT938436

EST:     CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAG                         AGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC
genomic: CTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGAC

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: 67

GATACAGAAGGTGTTCTTTTGCAACCTCTGCAATAAGCAGTACAAGCTGGCTCATGAATTTGAGAGTCACTTGAGCTCATATGACCACAATCATAGGAAGgtaatctgtt ... ttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG

Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 49

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 53

Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 44

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatttttctaatatatgttcatctgcatggttctgaataccttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG

         ttctaat  putative branch site (score: 44)
                                           ccttcgtc  putative PPT
     atttttctaatatatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctgttttgtgtacccttttgatttccctaatgaattgtatttgtatttttctaatatatgttcatctgcatggttctgaataccttcgtcgcagAGGTTTAAGGAAATGAGAGAAATGCAGAGCAGCAGTGGTAGTCGAGATGACAGACAGAAACGTGAACAACAACGAGAAGAGAAGGAGCTGGCAAAAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT