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

gtgaggccacctcggtcgcgaccgcgcagtggcggcccgatgtgtgtgagtgtggtttcgagttttttgactgggtgggttcccgattcgcatttcgttctctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA

Basic information

species	Zea mays
transcript	AC217358.3_FGT005
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 1

-------------------------gtgaggccacctcg-gtcgcgaccgcgcagtggcggcccgatgtgtgtgagtgtggtttcgagttttttgactgggtgggttcccgattcgcatttcgttctctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA
                         ||||         | |  ||    | |     | |   | ||| |||||  |||| ||| | |  ||  |  ||  ||  ||   |       ||  || ||| || |||||||||||| || || |||||| | |||||||||||| |||| ||||||||||||||||| ||||| ||||| |||||||||||||||||||| || ||||
gtaacccatcgatcgaagcctactagtgaacttgtgatgtgatgccgatgggtttcagagaagctatgcgtgtgcttgtgatttggtgggttgcgtttgaatgaattgttgtggttggttgtgtgctc-ggtgcagGTGTACCCTGAGGGGACTCACTTCATGATCCCGTGGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAA

upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 1

------------------------------------------gtgaggccacctcggtcgcgaccgcgcagtggcggcccg-------atgtgtgtgagtgtggtttcgagttttttgactgggtgggttcccgattcgcatttcgttctctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA
                                          |||| |  | | |||| ||||  |||| |  | |   |        ||| |||||  |||| ||| | |  ||     ||  ||  ||   |      |||  || ||| || |||||||||||| || || |||||  | ||||||| || | |||| ||||||||||||||||| ||||| ||||| |||||||||||||||||||| || ||||
gtaacgttccgtagcgccgtctagtagtgaacctgtgaacttgtgatgtgatc-cggt-gcgatggcgccgacgggtttcagagagctatgcgtgtgcttgtgatttggtgggttgcatttgaatgaattgttgtgattgattgtgtgctc-ggtgcagGTGTACCCTGAGGGGACTCAATTCATGATCCTGTTGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAA

upper sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 3

gtgaggccacctcggtcgcgaccgcgcagtggcggcccgatgtgtgtgagtgtggtttcgagttttttgactg-ggtgggttcccgattcgcatttcgttctctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA
     |   | |     ||       || |         || | |||   |    ||| |   |  || ||||   |   ||      ||  | || | |       |||||| || ||||| |||||||||||||||||||| ||| | || |||||  ||||||| || |||||  | || ||  | || || ||||| || || || |
---gagtttcttttcctgcat-----cactaattctgtaatttatgtttttcctattttg---tcattcactgtaattcattagaacatcatacttagatgggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTCATCTATGATGTCCGTACGCGCCCTCATCTTGTGGAGAGTACTTCAGGGA

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|149110344|gb|EE190366.2|EE190366

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|149076703|gb|EE165347.2|EE165347

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|15215048|gb|BI431144.1|BI431144

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|78081933|gb|DV510345.1|DV510345

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|148982739|gb|EE028558.2|EE028558

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|18659717|gb|BM500486.1|BM500486

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|149112958|gb|EE295743.2|EE295743

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|6021034|gb|AW065962.1|AW065962

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|6021466|gb|AW066394.1|AW066394

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|78084473|gb|DV512866.1|DV512866

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|31355780|gb|CD440137.1|CD440137

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|20507570|gb|BQ279689.1|BQ279689

EST:     GCGGACACCGTGCCATCGTCTTCATCCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|60398117|gb|DN230933.1|DN230933

EST:     GGGATC-AGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|148987626|gb|EE031500.2|EE031500

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|76011854|gb|DT939024.1|DT939024

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|22715353|gb|BU197718.1|BU197718

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|15214991|gb|BI431123.1|BI431123

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|78079465|gb|DV507877.1|DV507877

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|19436436|gb|BM952846.1|BM952846

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|31664014|gb|CD573194.1|CD573194

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|37418141|gb|CF646734.1|CF646734

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|6587642|gb|AW244960.1|AW244960

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|31356533|gb|CD440890.1|CD440890

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|6536621|gb|AW224934.1|AW224934

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

EST: gi|18649915|gb|BM498734.1|BM498734

EST:     GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAG                         GTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC
genomic: GCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATC

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: 447

CGGCGGCGCGGGGCTCTACGCCGTCCTCAACAGCTTCTACAACGTCGAGGGCGGACACCGCGCCATCGTCTTCAACCGCCTCGAGGGGATCAAGGACAAGgtgaggccac ... tctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttcgagttttttgactgggtgggttcccgattcgcatttcgttctctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA

         ttttgac  putative branch site (score: 296)
                                     tttcgttctct  putative PPT
     agtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggccacctcggtcgcgaccgcgcagtggcggcccgatgtgtgtgagtgtggtttcgagttttttgactgggtgggttcccgattcgcatttcgttctctggcgcagGTGTACCCCGAAGGAACTCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAA

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