ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacaccacatgtttatggtgcagtctgccttattgattctgattaagatttcaatactccatgaacacatctgctatttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG

Basic information

species	Zea mays
transcript	GRMZM2G093670_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13

-gtacaccacatgtttatgg---tgcagtctgccttatt----gattctgattaagatttcaatactccatgaacacatc-tgctattta-tgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
  ||    |  ||||| | |   |    | |   | ||     |||  |||||||   || |    | |||      ||  ||||  | | ||||||||||||||||  | || || ||||||||||||||||| || ||||||||||||||  | || ||||  || ||    || ||   |
gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 13

gtacac---cacatgtttatggtgcagtctgccttattgattctgattaagatttcaatactccatgaacacatctgctatttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
|||| |   || |    | | |||     | | ||   |  | | || |  | | |  |    | | |  |   |    ||  ||||||||||| | |||  | || |||||||||||||| ||||||||||||||||| |||||| | ||  |||   ||||| | |        
gtactcattcaaaaaaatctagtgacacgtactttg--gcattttatcattactcctctgtctcctcactaaggccaaaata-atgcagGCAGAAAATGCCCTGGACCAGATGGATTGGATGGAAAAGATAACTGGTGTAATTGCCACCTTATTGAGTGCACAAACACTG------

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 13

gtacaccacatgtttatggtgcagtctgccttattgattctga--ttaagatttcaatactccatgaacacatctgctatttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG-------------
           ||   |  | ||     | ||||   ||   |  ||  |  || |  | | | |  ||  |   |  |   ||||||||||| | |||||| ||||||||||||||||| |||||||||| ||| || |||||| | ||  |||     ||  | |  | |  |             
-----------gtacgtattccaa--aactttatcagtttaaagtttgggcatttatcattacttatactaa--aggaagcaatgcagGCAGAAAATGCAGTGGATCAGATGGATTGGATGGAAAAGATAAATGGAGTAATTGCCTCCTTATTGAGTGTCCAGACACTGGGAATGGTACGTAGTAGAT

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 15

gtacaccacatgtttatggtgcagtctgccttattgattctgattaagatt-tcaatactccatgaacacatctgctatttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
||    || |    | | |||   | | | ||     || | ||||    | ||  |    | | |  |   |    ||  ||||||||||| | |||  | ||||||||||||||||| ||||||||||||||||| |||||| | ||  |||   ||||| | |        
gtcattcaaaaaaatttagtgacatgtac-ttgcattttatcattacttctctctctgtctcctcactaaggccaaaata-atgcagGCAGAAAATGCCCTGGATCAGATGGATTGGATGGAAAAGATAACTGGTGTAATTGCCTCCTTATTGAGTGCACAAACACTG------

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 13

-gtacaccacatgtttatggtgcagtctgcctt-----attgattctgattaagatttcaatactccatgaacacatc-tgctattta-tgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
  ||    |  ||||  |       | |   ||     || |||  |||||||   || |    | |||      ||  ||||  | | ||||||||||||||||| | || || ||||| ||||||||||| || ||||||||||||||  | || ||||  || |||   || |||  |
gttatttaatgtgttctttagatttttttaattcatacatggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCACTGGACCAAATGGACTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAAATTCCTGAAAGG

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13

--------------gtacaccacatgtttatgg---tgcagtctgccttattgattctgattaagatttcaatactccatgaacacatctgctattta-tgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
              ||     ||    |||      |   || | | |  |||     | |||| | ||    ||||  ||   || | || |  | | ||||||| ||||||||| | ||||| ||||||||||| |||||||| ||||| ||||||||  |  | || |  || ||   ||| ||||||
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagtttt-cactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 13

---------------------------------------------------------------------------------------------gtacaccacatgttta-tggtgcagtctgccttattgattctgattaagatttcaatact--ccatgaac-----acatctgctattta-tgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
                                                                                             ||  |  ||   |  | ||||| | | |    | ||  |  |||||    | ||| || |   ||| ||      |||| ||||  | |   ||||||||||||||| | || || ||||||||||||||||||||||| || ||||||||  | || ||||  || ||  | || ||   |
gtaaatcttacagcttaggttgcactcatgaagttcagtttacttctttgaaattatttgatacctgaaactgtatttttgcttgatggttctgtgaaatactgatggaatggtgaattgttaagtgttattattgatttttttctcactagtgctcattaatgttgtacatttgcttgtcagcacagGCAGAGAGTGCACTGGACCAAATGGATTGGATTGAAAAGATAACAGGGGTTATTGCTTCATTACTGAGTTCTCAGGCTCCTGAGAGG

upper sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 13

------------------------------------------------------------------------------------------------gtacaccacatgtttatggtgcagtctgccttattgattctgattaagatttcaatactccatgaacacatctgctatttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
                                                                                                      |   |  | ||| ||  |  |   | | | |    ||  |   | ||   |||  ||    |||  ||      ||||||||||||| |||| | ||||| ||||| ||| |||||||||||||||| || || ||  ||||| |||  ||  |  | |  |||  |
gtacaaaatcaaaggttagatcaaaaatataaatttgggttttcattcatgtttttagactatacttatatgaagctcagcattatcagcccaaatacttgtccagtactaatgctggggattatgtcagt-acctagagcagattctctcaactttatattaacacttga-----atgcagGCAGAGAATGCACTGGATCAAATGGACTGGGTTGAAAAGATAACTGGAGTAATAGCTTCTTTGTTGAGTTCCGACGCACTTGAAAGG

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: 44 (upstream exon), 40 (downstream exon)
Score: 20

TGTAAATTTATTGACATCAACCATTAAAGTTGATGCTGAACAATCAGATCTGAGGTTCTGCTTCAGAATTTTTTCACCCACAAAAATCTACACATTGCAGgtacaccaca ... atttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG

Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 6

Block sizes: 41 (upstream exon), 43 (downstream exon)
Score: 6

Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 17

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattgattctgattaagatttcaatactccatgaacacatctgctatttatgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG

      ttctgat  putative branch site (score: 17)
           attaagatttcaata  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

RNA-Seq data