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

...aagtgaccgagagaaaactatctgtgccacttagtggtttgataaactatgttgtgataccaagttaccaacgttttgaaatcaataaatgttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA

Basic information

species	Zea mays
transcript	GRMZM2G300348_T04
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 3

---aagtgaccgagagaaaactatctgtgccacttagtggtttgataaactatgttgtgataccaagttaccaacgttttgaaatcaataaatgttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA
   ||   ||     ||||  ||||       ||| | | ||| | | || |  | ||| ||  |   ||   ||   |  ||  ||||  | ||  || ||||| |||||||||||||| ||||||||| ||   || || || ||||| || || || |||||||||||||||||||||||||||||||||||||||||||
gaaaacccacaattggaaacttatcatctgtcctttgagtttttacagaccacatggtg-tataataatat-gactaatcaaatgcaatgcacgt-atgccagCCTTTCAGGGACATGATAGAAGGGATGCGGTCAGACCTCAGAAAGACTAGATACAAGAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA

upper sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S323_70V6.1 (Physcomitrella patens), 3'ss of exon 3

------------------------------------aagtgaccgagagaaaac-tatctgtgccacttagtggtttgata--aactatgttgtgataccaag------ttaccaacgt-tttgaaatcaataaatg---ttgtgg------cagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA
                                     | |||||       |   ||   | ||   |||||  | || ||  |    | |     |||  ||      |||  ||  | ||   | |  |||  ||   || ||       |||||||| || |||||||| || ||||||||||  |||||   |||| |  ||||   ||||||||||||||||||| |||| |||||| ||||||| ||||
gtataaaatacattctcagtgcagcccaatcttcatgaatgacccctgcccactatagaggcgcaggttagtcatgtggtaggagtggtctcactttacttaggtttatttaggaagatgttctgagtttatacgtggctttctgaactatccagCCATTTAGAGACATGATCGATGGGATGAGGATGGATCTCGTGAAGTCCCGGTACGCCAACTTCGACGAGCTCTACTTGTATTGCTACAATGTTGCCGGAA

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|32792805|gb|CD945041.1|CD945041

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|91054433|gb|EB164851.1|EB164851

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|74241172|gb|DT649086.1|DT649086

EST:     TGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAA
genomic: TGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCC-ATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAA

EST: gi|148946928|gb|EC892212.2|EC892212

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGA
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGA

EST: gi|94472244|gb|EB701202.1|EB701202

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|148995759|gb|EE034988.2|EE034988

EST:     TGATGCCGCTCTCTCTGATACCATCTNCA-GGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGGATGAGGAGTGATC
genomic: TGATGCCGCTCTCTCTGATACCATCT-CAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGG-ATGAGGAGTGATC

EST: gi|78104640|gb|DV523058.1|DV523058

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|76911964|gb|DV164511.1|DV164511

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGGAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|76916879|gb|DV166586.1|DV166586

EST:     TGATGCCGCTCTCTCTGATACCATCTCCAAGGTCCCCCATAGACATTCCG                         CCCTTCAGGGACATGATTGAAGGGATGAGGAGT
genomic: TGATGCCGCTCTCTCTGATACCATCTC-AAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGT

EST: gi|71447701|gb|DR828751.1|DR828751

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGGAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|50325756|gb|CO520882.1|CO520882

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGGATGAGGA
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGG-ATGAGGA

EST: gi|93016198|gb|EB641718.1|EB641718

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGA
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGA

EST: gi|67028270|gb|CO457019.1|CO457019

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCC-ATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTANGAAGACAAG-
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|71444100|gb|DR825150.1|DR825150

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTG

EST: gi|149073532|gb|EE161835.2|EE161835

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGG

EST: gi|149075800|gb|EE164333.2|EE164333

EST:     TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAG                         CCATTCAGGGACACGATTGAAGGGATGAGGAGTGATCTTAGGA
genomic: TTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGA

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), 45 (downstream exon)
Score: 32

GTGGGAGAAGAGACTTGAGGATCTGTTCACGGGACGTCCTTACGACATGCTTGATGCCGCTCTCTCTGATACCATCTCAAGGTTCCCCATAGACATTCAGgtactgactg ... gttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 77

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 394

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

actatgttgtgataccaagttaccaacgttttgaaatcaataaatgttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA

                            ttttgaaatcaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgaccgagagaaaactatctgtgccacttagtggtttgataaactatgttgtgataccaagttaccaacgttttgaaatcaataaatgttgtggcagCCATTCAGGGACATGATTGAAGGGATGAGGAGTGATCTTAGGAAGACAAGGTATAACAACTTCGACGAGCTCTACATGTACTGCTACTATGTTGCTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA