ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatgaccactctctatctggttttacggttttag

Basic information

species	Zea mays
transcript	GRMZM2G107867_T04
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaata--caaaccttgcaa-caattagatt-------ctgttctggagttatgaccactctctatctggttttacggttttag-----------------------------
||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||||||||| ||||| || |||||||| || ||||||||| || | |||||| |  ||  || |||||| || |  |||  ||         || ||  |  |||      | |   | |  || |     |||                               
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagatag-atttatgtaggctagccagaccttgtaaactcttatgttgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgtttgtttggtgttccag

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaata--caaaccttgcaacaattagattctgttctgg-agttatgaccactctctatctggttttacggttttag-------------------------------------
||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||||| |||||||| ||||| || |||||||| || ||||||||| |  | |||||| |  ||  || |||||  || | |   || |||    |   ||  | |  |      |  |  | |||   || |                                       
GGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACGAGAATATCCCCAACCTATTCAAAAAGATAAAGgtgagataa-atttatgtaggctaaccagaccttataa-actcttatgctgactagatggtccttaaaatatctaagtttttattattattctgtatatttgagtatttgacctgcttgtttggtgttccag

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 6

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgt---gagaaagcacttatgtggaat--acaaaccttgcaa-caatta--gattctgttctggagttatgaccactctctatctgg----ttttacggttttag
 || ||||| ||||| ||||| || ||| | ||||| ||||||||||| || ||||| ||||||||||| |||||||| ||||| ||||| ||||| |||||   |  ||   | || | |  | |  |  ||    |  | |   |   || |   |||     |      |  |    || |||    |||| | | |    
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATGAAAATATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatttaattttatttatttaattaattgagtgatcggctgttgactacattcaaacatcccaggccttggacatgtggataattttccagct----

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatgaccactctctatctggttt--tacggttttag---------
 || ||||| ||||| ||||| || ||| | ||||||||||| ||||| |||||||| ||||||||||| || ||||||||||| ||||||||||| |||||   |     ||||  |  | ||  |   ||  |     |   |  | || |||  ||   |  |||     |    |||  |||   | | |         
AGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCCAATCTCTTCAAAAAAATAAAGgtactatttttcttaatttaattatta---ttatatttcctttttctttttatgggtttcaaaggactgatagttaaatttcctaccactgtcgtgtcaaatt

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtga-gaaagcacttatgtggaatacaaaccttgc--aacaattagattctgttctggagt-tatgaccactctcta---tctggttttacggttttag-
 || ||||| ||||| ||||| || ||| | ||||| ||||||||||| |||||||| ||||||||||| || ||||| ||||| ||||| ||||| |||||   |  |    | || |    ||   |  |  |  |   || || |  |||       | ||| |  |||  | |     |||   || || |     
AGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATGAAAACATTCCAAATCTCTTCAAGAAAATAAAGgtattgttaatgttaattttatttatttaattaactgagtgatcagctgttgtctacatatatattaaaactgcccaggccttggacatatggctaattt

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT5G39440.1 (Arabidopsis thaliana), 5'ss of exon 4

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtg--agaaagcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatgaccactctctatctggttttacggttttag
 || ||| |||||||||||||||||||  | ||||||||  | ||||| |||||||| || ||||| || |||||||| ||| | ||| | ||||| |||||   |  || ||   || |    || |||  |   |   |||| |    ||| || | || |   | || | | | | |              
TGTAGATATATGGAGTTGTGGGGTGATATTATATGCTCTGTTGTGTGGTACTCTTCCTTTCGATGACGAAAATATTCCTAATGTATTCGAGAAAATAAAGgtattaataaacaacgatctttt-tataaaaatcatatatattacacatggttatgaattttt--tctctatttctttag--------------

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaa----gcacttatgtggaa-tacaaaccttgcaacaattagattc-tgttctggagttatgaccactctctatctggttttacggttttag
 || |||||||||||||| || || ||  | || |||||  | || || |||||||| ||||||||||| || |||||||| || ||||| |||||||||||     |      ||||   |  |  || ||  ||      || | ||||| | |    | |   | ||   ||    | |  |||| |   |||||
AGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATTAAGgtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttct-ctttag

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaa-----agcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatg--accactctctatctg--gttttacggttttag---------------
 || ||||| ||||| ||||| ||||| || || |||||||| ||||| || ||||||||||||||||| || |||||||| || || || || || |||||          |   ||  | |    |  |        ||   ||  ||| | |  |  | || |   | ||| ||    |||     ||    ||||                 
AGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATGAAAACATTCCCAACCTTTTTAAGAAGATAAAGgtacattctattactcctcctctttcgtctatttgaactaatgcttgaattttttattttatttttcgtatcacccttcgactgtaaccttttttttttctcttttcgtcctatag

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 5

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtga----gaaagcacttatgtggaatacaaaccttgcaa---caattagattc-tgttctggagttatgaccactctctatctggttttacggttttag
||| ||||||||||| || || || ||| | || |||||||||||||| |||||||||||||||||||| || |||||||| || ||||| ||||| |||||       ||   ||||   |    |  |     ||| |    |  | |||     ||      || || ||  |  || | |  ||||  | ||  | 
GGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATGAAAACATTCCCAACCTTTTCAAGAAAATAAAGgtatttctaaatttacttcactaacttttagcatgtgccagcttagctggatctgcattgctcttttttgtccttttactttttatttttttgtttagaa

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: EFJ16445 (Selaginella moellendorffii), 5'ss of exon 4

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatgaccactctctatctggttttacggttttag
 || || |||||||| ||||||||||| || || || ||||| ||||| |  ||||| ||||| || || || ||||| ||||| ||||| ||||| |||||||   | || | |     || |  ||   |  ||   ||   |||| |||| |  ||||  |||                          
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtga---atcagtcagac--aacaagaagtcttaaatgtttt--ttcttttcttgt-ttattcccag-------------------------

upper sequence: GRMZM2G107867_T02 (Zea mays), 5'ss of exon 5
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 4

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagcacttatgtggaatacaaaccttgcaacaattagattctgttctggagttatgaccactctctatctggttttacggttttag
 || || |||||||| ||||||||||| || || || ||||| ||||| |  ||||| ||||| || || || ||||| ||||| ||||| ||||| |||||||   | || | |     || |  ||   |  ||   ||   || | |||| |  ||||  |||                          
AGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACGAAAACATTCCAAATCTATTCAAGAAAATCAAGgtga---atcagtcagac--aacaagaagtcttaaatgttt---tttttttcttgt-ttattcccag-------------------------

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|71437399|gb|DR818449.1|DR818449

EST:     CTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCNNNNNNNTTAAG                         GGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagc ... acggttttagGGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTG

EST: gi|60359581|gb|DN226554.1|DN226554

EST:     CTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCNNNNNNNTTAAG                         GGAGGTATCTACACACTTCCAAGT
genomic: CTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagc ... acggttttagGGAGGTATCTACACACTTCCAAGT

EST: gi|32930411|gb|CF035223.1|CF035223

EST:     TCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCNNNNNNNTTAAG                         GGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTG
genomic: TCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagc ... acggttttagGGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTG

EST: gi|211440538|gb|FL230375.1|FL230375

EST:     CTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCNNNNNNNTTAAG                         GGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTG
genomic: CTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagc ... acggttttagGGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTG

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: 46 (upstream exon), 46 (downstream exon)
Score: 65

GGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATGAGAATATTCCCAATCTGTTCAAAAAAATTAAGgtgagaaagc ... acggttttagGGAGGTATCTACACACTTCCAAGTCATTTGTCTGCTTTGGCCAGGGATTTGATCCCACGAATGCTTGTTGTTGAGCCTATGAAGAGAATCACAATTAGGG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114