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

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT

Basic information

species	Zea mays
transcript	AC189879.3_FGT003
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                            | |       | ||| |  ||    | |||  |||| || | ||  |       |   ||| || ||| |||||   ||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||| || ||||||||||||||||| || |||||||| ||||
----------------------------gtaaggctgag-catttctatggttacatggccatcattttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14

gtaaggctcattactactttccatttctgcatcaacatgtc-atattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                               | | ||| || | | || |  | | | ||  |    |||  |    |||    ||| |     ||| | |  |  |||||||| || || || || ||||| ||||| ||||||||||| || ||||||||||||||| | || ||  |||| || ||||| || |||| |  |   |
------------------------------gtaagcatttccaaactcctatataca-gctaagggatgtgctatgcttga---tatatactgaatacggtaatc-cagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 13

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctga-cagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                                      || |   |   |||  |      |  | |  || ||   |  | ||      || || | ||| |   |||||||| || || || || ||||||||||| ||||| ||||| |||||||| ||||||||| | || ||  | || |||||||| |||||||  |||   |
--------------------------------------gtaagtatttccaaagtcctttaacttatagct-ggccatatatttggtcttctgat-tactgttattcagGTTGTAGCCTCCCAGGACTGGCCAGAAGTGACAAAATATGCAGGATTGGTATGTGCTCAGCCTCATCGCGAGGAACTCATTCAAGACCTTTTTAAATGTT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 14

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggactta-tctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                            | |   |     ||  || ||||||   || |    |     ||  || |  ||| | | |   || | || |      ||||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||| ||||||| || || || ||  | || |||||||
----------------------------gtaaggattatacacttttatcaagtagtgga-gcatcgaaattcattat--actcagtttttttcttttgttttctttagGTTGTTGCTTCTCAAGACTGGCCTGAAGTGACAAAATATGCGGGTTTAGTTTGTGCTCAAGCTCACAGGCAAGAACTTATACAAGATTTGTATAAAACAT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 12

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
||||   |  ||  ||  |   ||   ||| ||       | | ||  ||   |  ||   ||    |       ||||    |     | |  | |  |  |   |||| || |||||||| || ||||| ||||| ||||| ||||| |||||||||||||||||||| ||| | || || || || || ||  | ||||| ||||
gtaaaatttctt--taactgatatca-tgcttcctagaaccttgtttttcctaaagtggttattgagg----aactttgttgctgatagattgttgtattaattgtagGTAGTAGCTTCTCAGGACTGGCCTGAAGTCACAAAATATGCAGGATTGGTTTGTGCTCAGGCTCACAGACAGGAACTGATACAAGATTTATACAAGACAT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                       |      || || |     ||||   ||| || | ||  ||  ||| |||  |    | | ||  || | ||         |||||| || || || ||||| ||||||||||| || ||||||||||||||||| ||||||||||| || |||||||| || ||||| ||  | || ||||| |
----------------------gtaaggatatgaaaac-ctgtatttcccaaaatctacagttccatgt-ttgagtccatattgattacaattat---------acagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 15

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                                                             ||  |  ||||     || |    |   |||||  ||||| | | |||||||||| || ||||||||||| || || || |||||||| ||||| ||||||||||| ||||| || ||||| || || || || || ||||| || |
-----------------------------------------------------------gtatgctgctcttc-cgctgcagccgtgaaactcaattgctgtt-atagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 14

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                                                      || |   |   || |  |  ||| |    | ||||| | |  |||   | ||||||||| |||||||| |||||||||||||| || || || || ||  | || || ||||| || ||| | |||||| | || || ||  | || |||||||
-----------------------------------------------------gtaagtgtacgatttttct--tttcgtgtgtctctcaataagctgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTAACGAAATACGCAGGTCTAGTCTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATTTGTATAAAACAT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 15

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgc-acatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                                                      |||||  | | |  |     ||  || |        |||||  ||||| | | |||||||||| || ||||||||||| || || || |||||||| ||||| ||||||||||| ||||| || ||||| || || || || || ||||| || |
-----------------------------------------------------gtatgctgcttttccgctacagtcgtgaa--------actcaattgctgtt-atagGTTGTTGCATCGCAAGATTGGCCCGAGGTGACGAAGTATGCGGGATTAGTTTGTGCTCAAGCACATCGTCAAGAACTGATACAAGATCTCTACAAGACCT

upper sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 14

gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
                                                     |  || ||   |||   ||   | ||    ||  | |    | |||   | ||||||||| |||||||| |||||||||||||| || || || || ||  | || || ||||| || ||| | |||||| | || || || || || |||||||
---------------------------------------------------gtaagtgtacgatttttcttttcgtgtgtctctaaataagc--tgtgcctgttacagGTTGTCGCTTCTCAGGATTGGCCAGAAGTCACGAAATACGCAGGTCTAGTGTGCGCTCAAGCTCACAGACAAGAGTTGATCCAAGATCTGTATAAAACAT

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|91877156|gb|EB407113.1|EB407113

EST:     ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCC                         GTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGCATGCTGGATTGGTT
genomic: ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT

EST: gi|21088909|gb|BQ401222.1|BQ401222

EST:     ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCC                         GTTGTTGCTTCTCAAGATTGGCCACAAGTTACAAAGTATGCTGGATTGGTT
genomic: ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT

EST: gi|211243806|gb|FL211917.1|FL211917

EST:     ACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCC                         GTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT
genomic: ACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT

EST: gi|211241581|gb|FL211915.1|FL211915

EST:     ACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCC                         GTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT
genomic: ACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT

EST: gi|9566493|gb|BE476002.1|BE476002

EST:     ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCC                         GTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT
genomic: ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT

EST: gi|20301316|gb|BQ164259.1|BQ164259

EST:     ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCC                         GTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT
genomic: ATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTT

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: 300

TTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACCCTGAAACCGGGGAGGACTCAAGTCCATCAATCGCTGCCgtaaggctca ... ctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 90

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 39

Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 51

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT

                               atctcac  putative branch site (score: 51)

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggctcattactactttccatttctgcatcaacatgtcatattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA