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

gtctatctcctactctaaaatgcaagcatgtactaatcaaccctgggggaaatgtcttctgtttttttttgtggcaacatctttccatactgatgtgacaatttgttccccctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC

Basic information

species	Zea mays
transcript	GRMZM2G124353_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 5

gtctatctcctactctaaaatgcaagcatgtactaatcaaccctgggggaa-atgtcttctgtttttttttgtggcaacatctttccatactgatgtgacaatttgttccccctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC
       || |   | || |  ||  ||| |   |||  ||| |||   || | | ||      |||  || ||    |||  ||   | |||||||         ||     || ||  |||||||||| ||||| |||||||||||||||||||| ||||| || |||||||||| |||| | || |||||||||||||||||||||||||||||||| |
------gtcttcacccaacacacatacatttg--aatggaccttggaaaaataagcctcaaaggtttaattttgttgccattatttattgctgatgtt--------ttttttttgtttgtagGGAATTGGAAATGGTCTACCATTGGGGGCAGTTGTAACAACACCCGAGATTGCAAATGTGCTGGCGCAAAAAATCCAATTTAACACATTTGGTGGAAACC

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G31630.1 (Glycine max), 3'ss of exon 5

gtctatctcctactctaaaatgcaagcatgtactaatcaaccctgggggaaatgtcttctgtt--tttttttgtggcaacatctttccatactgat--gtgacaatttgttccccctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC
                            | | | |     |  || || || | | || |  |   |||||       | |||||    | ||  |   | | |  | ||      | || |||||| ||||||||||| || |||||||| || || || |||||||| || |||||||||||| | || ||||| || |||||||| || |||||||| || |
-------------------------ttttctgccatatttcattgtggaaattattttgttctaactttttaaccttcatatcttctgctgctatttcatcatatctcgtgttaatttgtatcagGGTATTGGCAATGGTCTGCCATTGGGAGCTGTAGTTACAACTCCAGAAATTGCAAGTGTGATGGCCCAAAAGATTCAATTTAATACCTTTGGTGGGAACC

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G14850.2 (Glycine max), 3'ss of exon 5

gtctatctcctactctaaaatgcaagcatgtactaatcaaccctgggggaaatgtcttctgtttttttttgtggcaacatctttccatactgat--gtgacaatttgttccccctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC
                            ||   || |  |   |||     || |  |      |||||       | || ||    | ||  |   | | |  |  |      | || |||||| ||||||||||| || ||||| || || || || |||||||| || |||||||||||||| || ||||| || |||||||| || |||||||| || |
-----------------------ttttctgccatattttattatggaatttattttgttctcactttttaaccttcatatattctgctgctatttcatcatatctcatgttaatttgtatcagGGTATTGGCAATGGTCTGCCATTAGGAGCTGTAGTTACAACTCCAGAAATTGCAAGTGTGTTGGCCCAAAAGATTCAATTTAATACCTTTGGTGGGAACC

upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0031g01330.t01 (Vitis vinifera), 3'ss of exon 5

-----------------------------------------------------------------------------gtctatctcctact--ctaaaatgcaagcatgtactaatcaaccctgggggaaatgtcttctgtttttttttgtggcaacatctttccatactgatgtgacaatttgttccccctggtt-tcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC
                                                                              | | | || |  |  ||    | | || ||| | ||  ||||  |      | | | || | |  | | ||||   || ||   || |   |        | ||            || |||||| |||||||||||  ||||||| || ||||| |||||||| || || || |||  ||| || ||||| ||||| ||||||||||| || ||||| || |
gtttctctagtcatccttatagtcttttatggtttttacccatcctgggtggcattgatagtaaaattctatattgcatttctttcttggtaacttgttttctag-atgcatta--caactttcatttcagtttattatttcatgtcttgtaa-aatattgctcaaccattccactgaatttcagaaataacatttatcagGGCATTGGCAATGGTTTACCATTAGGAGCAGTGGTGACAACACCAGAAATAGCAGATGTATTGGCTCAGAAAATTCAATTTAACACTTTCGGTGGGAACC

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|211311887|gb|FK975958.1|FK975958

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

EST: gi|32942110|gb|CF046929.1|CF046929

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

EST: gi|30031577|gb|CB833428.1|CB833428

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

EST: gi|32943504|gb|CF048323.1|CF048323

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

EST: gi|60338215|gb|DN205188.1|DN205188

EST:     GGGGATT-CAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

EST: gi|44682053|gb|CK787101.1|CK787101

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

EST: gi|94472312|gb|EB701270.1|EB701270

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGAC
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGAC

EST: gi|13558145|gb|BG549501.1|BG549501

EST:     GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGC
genomic: GGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGC

EST: gi|113701983|gb|EE679487.1|EE679487

EST:     GGGATTCCAGACACAAGGTGTCATTCTTGACATAGTCACCATGGCAAAG                         GGAATTGGCAATGGCTTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT
genomic: GGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATT

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: 225

TATTGCTGATGAAGTCCAGAGTGGTTTTGGCCGTACTGGCAGTCATTACTGGGGATTCCAGACACAAGGTGTCATTCCTGACATAGTCACCATGGCAAAGgtctatctcc ... ctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 422

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 543

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 202

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtggcaacatctttccatactgatgtgacaatttgttccccctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC

                     tactgat  putative branch site (score: 202)
                                       ttccccctggtttc  putative PPT
                                 aatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatctcctactctaaaatgcaagcatgtactaatcaaccctgggggaaatgtcttctgtttttttttgtggcaacatctttccatactgatgtgacaatttgttccccctggtttcagGGAATTGGCAATGGCCTACCATTGGGGGCAGTTGTGACAACTCCTGAGATTGCAAGTGTGTTAGCTCAAAAAATCCAATTTAACACATTTGGTGGAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA