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

...gaccattgctcaatgtcttatttctgtgtttctcagtagtaattatagctcacattgttagccttcagctaacacttctgttttttatcctatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG

Basic information

species	Zea mays
transcript	GRMZM2G050371_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 3'ss of exon 4

------------------------------------------------gaccattgctcaatgtcttatttctgtgtttctc---agtagtaattatagctcacatt--gttagccttcagctaacacttctgttttttatcctatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG
                                                 ||   |  |  |  |  ||| || ||  | |||   | || ||  |  |  |   ||   | ||    |    |  || | || | |||  |  | |  ||||||||||||| ||  |||||||||| ||||| ||| | |||| ||||||||| ||||||||||||||||||||  | ||||| || |||||||||||||| |
gttagaatacctccttttatgctcttgttccgatgttctgtctgcacaaactcattttacacataatatctcagtagtcctctccactattatctgcatatgggatctggctaatactttattctcaatactttgtttctttgt-tcctgcagGTGGATGAAGCTATGATGGAGATGGCTGGGCCAAATGCCTTCCTTATGCATTGTTTGCCTGCAGAGAGAGGGATAGAGGTAACAGACGGCGCCATTGAAG

upper sequence: GRMZM2G050371_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G75330.1 (Arabidopsis thaliana), 3'ss of exon 4

gaccattgctcaatgtcttatttctgtgtttctcagtagtaattatagctcacattgttagccttcagc-taacacttctgttttttatcctatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG
     |      | || | || |   |   | |  || | |||  | | |    ||  ||   | ||      |||   |   | ||||  |  ||||||||||||||| || |||||| || | || || | | | |||||  | ||||| ||||||||||||||||||||||| ||||||||  | || | | | ||||
----gtaaacataagtttaatctggcttagttttggt-gcaatgctcggtactcttactaaattacactgcttcacgcttacatattatgttcaattgcagGTGGATGAAGCTCTGATGAAGTTGGCGGGTCAAAAAGCCTATTTCATGCATTGTTTGCCTGCAGAGAGAGGAGTTGAGGTGACCAATGGAGTCGTAGAGG

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|93014508|gb|EB640028.1|EB640028

EST:     ACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGGCA
genomic: ACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTAT-GCA

EST: gi|60341228|gb|DN208201.1|DN208201

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTTGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|67018434|gb|CO447183.1|CO447183

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|5499140|gb|AI855007.1|AI855007

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|91869686|gb|EB400489.1|EB400489

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTCCCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|116817077|gb|EC859881.1|EC859881

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACA                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|78024536|gb|DV492923.1|DV492923

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|211230727|gb|FL437690.1|FL437690

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|50326082|gb|CO521208.1|CO521208

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|78077353|gb|DV505787.1|DV505787

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTCCCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|78125153|gb|DV543537.1|DV543537

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|16925839|gb|BM078907.1|BM078907

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|8930470|gb|BE225234.1|BE225234

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCGCG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|71758049|gb|DR955986.1|DR955986

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|149072339|gb|EE160609.2|EE160609

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|32832854|gb|CD972532.1|CD972532

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|60394172|gb|DN227042.1|DN227042

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|32910603|gb|CF015415.1|CF015415

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

EST: gi|71760816|gb|DR958753.1|DR958753

EST:     GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

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), 48 (downstream exon)
Score: 91

AGCAGTTAAGGGAGCAGACATTGTGTACACAGATGTTTGGGCCAGTATGGGACAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtatgtttgt ... tatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tagctcacattgttagccttcagctaacacttctgttttttatcctatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG

                     agctaac  putative branch site (score: 71)
                             cttctgttttttatcc  CT-rich tract
                                   ttttttatcctatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaccattgctcaatgtcttatttctgtgtttctcagtagtaattatagctcacattgttagccttcagctaacacttctgttttttatcctatattgcagGTGGATGAGGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCACTGTTTGCCTGCAGAGAGAGGAGTGGAGGTGACTGACGGCGCCATTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- ccattgc
- - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - -gctcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcagc