ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctctctaatacatttcatttccattgctctttgaggcattaccaattatattttcaggttgctttagagtagatatttctattgggttttagtt...

Basic information

species	Zea mays
transcript	GRMZM2G014454_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G014454_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g62070.3 (Oryza sativa), 5'ss of exon 4

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtct-------ctctaatacatttcatttccattgctctttgaggcattacc----aattatattttcaggttgcttt------agagtagatatttctattgggttttagtt-----------------------------------------------------------------
||||||||||| ||||| ||||||||||| || |||||||||||||| || |||||||||||||| || ||| ||||||||||||||||        | |  |    || |  |||    ||| ||  |   ||  |    || | |   |   | || ||||      |   ||  | | | |  ||  | || | |                                                                 
GGAATACTTGTCTTTGCCTCTGTTATGGCGACACTTGGCCTTCAGATCATCCTAGAATCAGTACGCTCGTTGTTGTCTGATgtaagtctgctgatgttttgttggccttgaactcctactctcattttgcttttgaccagaaactttgcctgaggatttcttttctagaacgataagtgtctttgatgtttgttggctttgaaattctgttgtagcttgccatatacctttctgattgctgaacttattgtcttgttctccag

upper sequence: GRMZM2G014454_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA02G10580.1 (Glycine max), 5'ss of exon 4

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtc--tctctaatacatttcatttc-----cattgctctttgaggcattaccaattatattttca---ggttgctttagagtagatatttctattgggttttagtt----------------------
||||| ||||||||||| ||||||||||| || ||||| || ||||||||  | || ||    ||  ||||  | |||  |||||||   |   |  |  ||||| ||         |  |||    |   || |   | || |||||||    ||||||  |       ||||||||     || || |                       
GGAATTCTTGTTTTTGCCTCTGTTATGGCGACACTTGGACTGCAGATAATCTTGGAGTCTACCCGCACATTAATATCTTCTgtaagttgattcttgctctatttctttaggcaaatctgactcccaaactgataaaacaataaattttcatttagttgctggatctcttttatttctaggtatttctaatgtgtctcataatgacatttccag

upper sequence: GRMZM2G014454_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA18G52280.1 (Glycine max), 5'ss of exon 4

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtc--tctctaatacatttcatttc-ca---ttgctctttgaggcattacca-attatattttca---ggttgc-tttagagtagatatttctattgggttttagtt-------------------------
||||| ||||||||||| ||||||||||| || ||||| || ||||||||  | || ||    ||  ||||  | |||  |||||||   |   |  |  ||||  ||   ||    ||       |     ||  | |||| |||||||    ||||| |||||  |   | ||| |  | ||| ||  |                          
GGAATTCTTGTTTTTGCCTCTGTTATGGCGACACTTGGACTGCAGATAATCTTGGAGTCTACCCGCACATTAATATCTTCTgtaagttgattcttgctctatttttttaggcaaatctgacacccaaactgctaaaacattaaattttcatttagttgcatttaggatctcttttttttctaggtatttctaatgtgtctcgtaatgacatttccag

upper sequence: GRMZM2G014454_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv13s0019g00020.t01 (Vitis vinifera), 5'ss of exon 4

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctctctaatacatttcatttccattgctctttgaggcattaccaattatattttcaggttgctttagagtagatatttctattgggttt-tagtt------------------------------------
||||| |||||||||||||||||||||||||| || || || ||||||||  | || ||||||||  || |    ||||| ||||||  |  | ||  | |||| ||  |||  | |  || | |       | |||  |  |  || |||||    |  | |    | ||   |  | |||                                    
GGAATCCTTGTTTTTGCTTCTGTTATGGCAACTCTGGGACTGCAGATAATCTTGGAGTCAGTACGCACACTATCATCTGACgtaagtggc--tgatctaattcaatt--attagtgtaagaaggaacctttttcatagatgaattttactttaattcatttgtgaacaatgaactaatggttatcaatctgtcatataaataatgtgtcctttcccag

upper sequence: GRMZM2G014454_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S11_299V6.3 (Physcomitrella patens), 5'ss of exon 5

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctctctaata---catttcatttccattgctctttgaggcattaccaattatattttcaggttgctttagagt----agatatttctattgggttttagtt-------------
|| || || ||||||||||| || |||||||| ||||| ||||| || ||||||||||| |||||  |  |  |  || | ||||| | | |  |||   || || ||  ||  ||||     | |  |||   ||| |||| | |  ||| |  |  ||       || || ||  |    | |  |             
GGTATTCTGGTTTTTGCTTCAGTAATGGCAACACTTGGTCTTCAAATCATTCTAGAATCCGTACGGACTCTAATCACTCAGgtaagacacacacataggtcactttatagcctctgcttcgctatg-gttaattattctattcttaatttgttggaatgttttggattacttataacgaaaatgaaatttttgacttacag

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|91050036|gb|EB160454.1|EB160454

EST:     CCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT                         GGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATC
genomic: CCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctct ... aattctccagGGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATC

EST: gi|91056110|gb|EB166528.1|EB166528

EST:     CCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT                         GGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATC
genomic: CCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctct ... aattctccagGGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATC

EST: gi|148945796|gb|EC891082.2|EC891082

EST:     CCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGAT                         GGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATC
genomic: CCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctct ... aattctccagGGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATC

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: 16

GGAATACTTGTTTTTGCTTCTGTTATGGCAACCCTTGGCCTTCAGATAATTCTAGAATCAGTACGTTCATTGGTGTCTGATgtaagtctct ... aattctccagGGAGATGAATTCAGCTTAACAAGTGATCAAGAAAAGTGGCTTGTGGACATCATGCTCTCCGTGACATTGGTAAAACTTGCCCTGGTTATATATTGCCGCT

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 51

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72