ERISdb: a Database of Plant Splice Sites

General
Orthologs
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgtgcttgtgttcacttcttatcatgtaattatggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaaacaataccttaattagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA

Basic information

species	Zea mays
transcript	GRMZM2G320615_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 3

gtttgtgcttgtgttcacttcttatcatgtaattatggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaa--actgtagtgtgccttttatttttatattgaaaacaatacc-----ttaattagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
              | | |  |  |  |||  |     || | | |  |    ||| |   |  |   | ||| ||||    ||||||||  |    |||||| | |  | ||| |||| || ||| ||    || |      |||||  ||  ||| | ||||||| |||||||| | ||| ||||||| ||  |||| |||||||||||||||||| ||||||| ||||| | ||||||| |||||||||||||
-------------gtaaataatggttttgtgctc----cccagtcttttctatcatgcccattataaatattatcctaccagatatgtatccaggttactgtactataacctttcttttaatgttgtaagttgtatcaagtgctaattgtttggttctaacagGGAAGAGTTAGAAATCTTTTCAAAAGAAGTTGTTCGATTTGGAAATCGTTGCAAGAATCCTCAATGGCACAGCTTGGACCGCTACTTTGAAAA

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G33040.1 (Glycine max), 3'ss of exon 2

gtttgtgcttgtgttcacttcttatcatgtaattatggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgt-atggaaaactgt---agtgtgccttttatttttatattga-aaacaataccttaattag-ttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
                            ||||  |      |||| ||| |   |||| |  |  | | |    |   ||||  |  | |   | |||| |   ||| | ||     ||| || | ||| ||||  ||  | | || | || ||     ||||||  ||||  |||| ||| |  | ||||| ||||| |||||||||||||  ||||||||||||||||| ||||||||| | |||||||| ||
----------------------------gtaac-actattgaattaaatcaa--attcctaacaaggggggcttctgtttcatgacctgaccaacaactattttagtttaccaggactttataaaatgataaactttatgtgattttgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G16690.1 (Glycine max), 3'ss of exon 3

gtttgtgcttgtgttcacttcttat-catgtaattatggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaaacaataccttaatt-agttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA-------
                      |||  ||   ||||   |  | |  ||  | |   |  |||        | | |  | |   |   | |     | |    ||   ||   |  |||| |||  || |  ||  | | ||  | | ||    ||||| || |||| ||||| ||| | || ||||| ||||| |||||||||||||  ||||||||||||||||  ||||| ||||| |||||||| ||       
---------------------gtatatattggattaaatcaaattacaaagaacggcttctgtaccatcaataaactaactattttattgttttgcattaccatgactctagaaaatttaaatttcaa-ctgtatgtgattttggattatgttgtcagGCAAGAGTTGGAAGTTTTTTCTAATGAGGTGATTCGTTTTGGAAATCGTTCGAAGGATCCTCAGTGGCGCAACTTAGACTGTTACTTTGAGAAACAAACC

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 1

gtttgtgcttgtgttcacttcttatcatgtaattat-ggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaa-----acaataccttaatt-agttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
                            |||| ||| ||  ||| | || |  | |  | || | |   |  ||    ||    ||  |||   |   | | |  |     | | | | ||||| |||     ||  ||  | | ||  | | |     ||||| |  ||||  | || ||| |  | ||||| ||||| |||||||||||||  ||| ||||||||||||| ||| | ||| | |||||||| ||
----------------------------gtaaatattggattaaatcaaattactaagcatggcttctttactatga-ataagctaactattttatttttttgcattatcatgactctaatattaaaatttcaactgtatatgattttggattacgttgtcagGCAGGAGTTGAATGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACCTAGACCGTTACTTTGAGAA

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G00670.1 (Glycine max), 3'ss of exon 2

gtttgtgcttgtgttcacttcttatcatgtaattatggcct--aatttaattatccattcttgtcgtgcgtgttaccctattcaat-atgtatggaaaactgtagtgtgccttttatttttatattga-aaacaataccttaat-tagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
                            |||| ||| |  |  | |  ||||    | |   |  |    |||| |   |       |  | |  |  | | |||| | ||  |  ||| || | ||  ||||  |   | | | |  || ||     ||||||  ||||  |||| ||| |  | ||||| ||||| |||||||||||||  ||||||||||||||||| ||||||||| | |||||||| ||
----------------------------gtaactattgaattaagtcaaattcctaactaggggggcttctgtttcataacaaggccaactttaaactattttagtttaccactactttataaaatgctaaactgtgtgtgattatgatttatgtttccagGGATGAGTTGAAAGTCTTTTCTGATGAGGTAATTCGTTTTGGAAATCGTTCAAAGGATCCTCAGTGGCACAACTTGGACCGATACTTTGAGAA

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 2

gtttgtgcttgtgttcacttcttatcatgtaattat-ggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaaacaataccttaa------ttagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
                            |||| ||| ||  ||| |||| |  | |  | || | |   |  ||    ||    ||| |||   |   | | |  |  |  | | | | ||||| |||   | ||  ||       || |   ||    ||||| |  ||||  |||| ||| |  | ||||| ||||| |||||||||||||  ||| ||||||||||||| ||||| ||  | |||||||| ||
----------------------------gtaaatattggattaaattaaattcctaagcatggcttctttactatga-ataagctatctattttattgttttgcattaccatgactctaatattaaaatttaaactgtatgagattttggactatgttgtcagGCAGGAGTTGAAAGTTTTTTCTGATGAGGTGATTCGTTTTGGAAATCGTTCAAAGAATCCTCAGTGGCACAACTTAGAGCGTTACTTTGAGAA

upper sequence: GRMZM2G320615_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 2

gtttgtgcttgtgttcacttcttatcatgtaatta-tggcctaatttaattatccattcttgtcgtgcgtgttaccctattcaatatgtatggaaaactgtagtgtgccttttatttttatattgaaaacaataccttaattagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA
                            || | || ||    |   |||||     |  || |      |||||      ||| | | |   |   | | |  |     | ||||| | | | |||||    |  ||| |||    ||||    ||||||| |  |  || | ||| |   ||| ||  | || ||||| ||||| || || |||||||||||||| ||||||||| | |||||||| ||
----------------------------gtgaatactgaaacagaataattgctt-tgattatatcatttgttaatgggctcattttttcctggttatttt--tccaattgttattctaaaagtgaaa-tggtcacttcattttccaattatggcagGGAAGAACTGAAAATTTTTTCTGGAGAAGTGGTCCGTTTTGGGAATCGATGTAAAGATCCTCAGTGGCACAACTTGGACCGTTACTTTGAGAA

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: 39 (upstream exon), 23 (downstream exon)
Score: 6

TACAGAGTTATGCAGAAGGTGCGTCCTACCAATCATTTTGTTATATCCAAAGATTTTGATGAACTGCTCAAGATGGCAACTGCCGACAAAAGgtttgtgctt ... attccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA

Block sizes: 39 (upstream exon), 15 (downstream exon)
Score: 3

Block sizes: 47 (upstream exon), 20 (downstream exon)
Score: 6

Block sizes: 38 (upstream exon), 31 (downstream exon)
Score: 2

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgccttttatttttatattgaaaacaataccttaattagttaattccatcagGGAAAAGTTAGAAGTATTTACAAAAGAGGTCATTCGCTTTGGAAATCGTTGCAAGGATCCTCAGTGGCATAACTTGGACTGCTACTTTGAAAA

                                        agttaat  putative branch site (score: 2)
                                              ttccatc  CT-rich tract
       ttttatttttatattg  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

RNA-Seq data