ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGGGCTGTGAATCTGATGGCCGACGTAGTCCAAGAAGAACACATAAACAAGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcattgtgctgatacgatagcgattagcaaactatcaatatatacttcacccatcacaatgatgctaactatagcacgcttacaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G113073_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G113073_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G22400.1 (Arabidopsis thaliana), 5'ss of exon 4

CTGGGCTGTGAATCTGATGGCCGACGTAGTCCAAGAAGAACACATAAACAAGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcattgtgctgatacgatagcgattagcaaactatcaatatatacttcacccatcacaatgatgctaactatagcacgcttacaatgcag
 |||||  | ||||| ||||| || || || ||  | |||||  |||||||||||||    ||||| || |||||||| ||||||||||||||||| |||||     | | |||    || |    ||||| |||  | | | |         |      | ||||||      |     || |||  | || ||
TTGGGCCATCAATCTAATGGCAGATGTTGTTCAGTATGAACATCTAAACAAGATGAATTCACGCAACATCGCTATGGTTTTCGCACCAAATATGACACAGgtg----agtctgcaacaacaaggttgattatcaatgtttaactcggggtcagatgggataaaatgat------tgagaaacacttgtattgtag

upper sequence: GRMZM2G113073_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv06s0080g00580.t01 (Vitis vinifera), 5'ss of exon 4

CTGGGCTGTGAATCTGATGGCCGACGTAGTCCAAGAAGAACACATAAACAAGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcattgtgctgatacgatagcgattagcaaactatcaatatatac-ttcacccatcacaatgatgctaact--atagcacgcttacaatgcag-------
 |||||  | || || ||||| || || ||||| || || ||  ||||||| ||||| |  ||||| ||||| |||||||| |||||||| |||||||||||   |     || |  |||| |      | | ||| | || |  ||    ||  |   ||   ||||   | | |  |||  ||| |  || ||||        
TTGGGCCATCAACCTCATGGCAGATGTCGTCCAGGAGGAGCATCTAAACAAAATGAATGCACGCAACATTGCAATGGTCTTTGCACCAAACATGACTCAGgtgaggttgaatggtt-tacgct----tcttgaaaattgtccaagtagggatttgcatgtccagatgaaattgaatgaatatgacgttctcattgcattttaaat

upper sequence: GRMZM2G113073_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 5'ss of exon 4

CTGGGCTGTGAATCTGATGGCCGACGTAGTCCAAGAAGAACACATAAACAAGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcattgt--gctgatacgatagcgattagcaaactatcaatatatac--ttcacccatcacaatgatgctaactatagcacgcttacaatgcag--------------------------------
||||||||| ||| ||||||| || ||||||||||| |||    | ||||||||||||| |||||||||||| |||||||| || || |||||||||||||||   |||  |   |     |  | |    | |||    |  |  || |||  ||      ||||  |    || | | | | ||||| ||  || ||                                
CTGGGCTGTCAATTTGATGGCTGATGTAGTCCAAGACGAAGTAGTCAACAAGATGAACGCTCGCAATATTGCAATGGTCTTTGCTCCTAATATGACTCAGgtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaac--tgaagcctaacacctgtttcgacctctatatctgcag

upper sequence: GRMZM2G113073_T01 (Zea mays), 5'ss of exon 4
lower sequence: PP1S1_829V6.2 (Physcomitrella patens), 5'ss of exon 5

CTGGGCTGTGAATCTGATGGCCGACGTAGTCCAAGAAGAACACATAAACAAGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcattgtgctgatacgatagcgattagcaaa--ctatca----atatatacttcacccatcacaatgatgctaactatagcacgcttacaatgcag-------------------------------------------------------------------------
||||||  | ||  |||||||||| || ||  |    ||     | ||||||||||| | |||||||||||| ||||| ||||| || |||||||| ||||||| |     | |||    | |  | ||  | | |  || |          ||  | | |   |  ||   ||| |||||  ||   |||||   |  |                                                                          
CTGGGCCATTAACTTGATGGCCGATGTCGTGGAGCTGGAGTCTTTCAACAAGATGAATGCTCGCAATATTGCAATGGTATTCGCTCCTAATATGACACAGgtatggagcacttctgcagtggtctctatctgtagaagctgttgtatggcgaatggtcctcttttttcac--atggtaactcaagattgcttatcctaaaaggtggttttccgttagcatgttatgtgtcaatgaaggttatccctttactgattcatatttactgccctgcag

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|86473813|gb|DY240183.1|DY240183

EST:     AGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAA                         ATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGATTTTT
genomic: AGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTT

EST: gi|60396528|gb|DN229397.1|DN229397

EST:     AGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAG                         ATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTT
genomic: AGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTT

EST: gi|5650020|gb|AI920380.1|AI920380

EST:     GATGACCGATCGCAATATTGCTATGGTCTTCGGCACCAAATATGACTCAG                         ATGCCAGATCCTT
genomic: GATGAACGATCGCAATATTGCTATGGTCTTCG-CACCAAATATGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTT

EST: gi|60355630|gb|DN222603.1|DN222603

EST:     AGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAG                         ATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTT
genomic: AGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTT

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: 49 (upstream exon), 45 (downstream exon)
Score: 45

CTGGGCTGTGAATCTGATGGCCGACGTAGTCCAAGAAGAACACATAAACAAGATGAACGATCGCAATATTGCTATGGTCTTCGCACCAAATATGACTCAGgtattgcatt ... tacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58