ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtacttgtttttctagatagtgtgctaccctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgattgcag

Basic information

species	Zea mays
transcript	GRMZM2G178102_T01
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtacttgtttttctagata---gtgtgctaccctaatatggtgatgcacctgatgttgatatc--tctgaccgtttcaaacgtgatactgattgcag
||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||| | |||||||||||||||||||||||||||||||| | ||| | | ||| |   |||   ||   | || |  |  | |   | |||||  | |   ||  | |   | ||| |  |   ||||| |||
TCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAGgtaatgtattcgttgtacaagaaaactgtgcagtatgttgattttctctttccattcatgttttttttgttcaaatcaactgaaatgaaaatttgattacag

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G13110.1 (Glycine max), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgta------atgtacttgtttttctagatagtgtgctaccctaatatggtg-atgcacctgatgttgatatctctgaccgtttcaaacgtgata-ctgattgcag
||| || || |||||| |||||||  |||| | |||| | || || || ||||||||||||||||||||||| |||||| |||||||||||||       ||  | |  || ||||  || ||    | |    |||      ||| |  || | |   ||| | |  || | |||    |  |  ||   || ||
TCTTCTTGCAATTGCTCAGGAGACCCTGGCGGCGTTCCTTTCAAAAGCTACTGGAACTGCTGTCAACTGGGTCCAAATGATTGGGATGAAGgtgtgacctattcaataattcttcttcatggt-cattgcttgcataaaacatatgtatttg-tatgattatattttgcc-tctcattttttctgtcttcgtgtag

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G13640.1 (Glycine max), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaa--tgtacttgtttttctagatagtgtgctacccta-atatggtgatgcacctgatgttgatatctctgaccgttt--caaacgtgatactgattgcag--
||| ||||| || |||||||||||  ||||||||||| | |||||||| ||||||||||||||| ||||||| || ||| ||||||||||||||     |  ||  | ||||  || |  ||      ||  |||  |     |  |  || |  | |   ||   ||||    |  |||||  | | ||     
TCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtatgccctttttaatattcttaattgcttgtgtttgtatgtatatttcataaatttgtgatattgttgttgtgtgtttgttcattgtgattttcaatgagtag

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G02750.1 (Glycine max), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatg-------tacttgtttttctagatag--tgtgctaccctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgattgcag--------------
||| ||||| || |||||||||||  ||||||||||| | |||||||| ||||||||||||||| ||||||| || ||| |||||||||||||||||       || |  | |||   | | |  | |  | |  |  |||| |  |  |  | ||    |||| | | |  |||       |  |  | ||||||               
TCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtaatgccccgtttaataatctttgatgcttggttttttttctttcttatgtttgtataattcata--aatatttgttaatgttgttgtgtttttgttaattgcaatttgcaatgaatag

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA05G30000.1 (Glycine max), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtacttgtttttctagatagtgtgctaccctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgattgcag
||| || ||||||||| |||||||  | |  |||||| | ||||| || ||||||||||||||||||||||| || ||| |||||||||||||| ||  ||  || |||  | |  |    | |   |||||  || |  |    ||  |  | |  || |   ||||   | | ||   |       
TCTTCTTGCTATTGCTCAGGAGACCCTAGTGGAGTTCCTTTCCAAAGCTACTGGAACTGCTGTCAACTGGGTCCAGATGATTGGGATGAAGgta-tgacctacttcttcatggtcattgcttgcataaatatattggtata----attatattttgcctcattttttctgtcttaatgtag-------

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatg--tacttgttt-----ttctagatagtgtgctacc------ctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgattgcag------
 || ||  |||| || |||||| |  | ||||||||| | |||||||| || |||||||||||  ||||||| || ||| ||||||||||||||||   | || |  |      |||  |   |||   | |      ||| | |   | ||   |||| | |||  |   | |   ||         |   | ||||| |      
ACTCCTTTCTATAGCAGAGGAGGCCCTAGCAGAGTTCCTTTCCAAGGCTACAGGAACTGCTGTTGACTGGGTTCAGATGATTGGGATGAAGgtaatactttctggcctgaatactcttaaagttgtataatctgatttctattctttagttgtgtctgaagatgaagttgtttatgattatttgatgaaccttcattgctggtgtag

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgta-atgtacttgtttttctagatagtgtgctaccctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgattgcag
||| ||| | ||||| |||||||| ||||| |||||| | | |||||| || |||||||||||| ||||||| || ||| |||||||||||||| ||    |    | | |  |   | |  ||     | |||  |  |    |        | |   |     |||    | || |  ||  || ||
TCTTCTCTCGATTGCGGAGGAGACCTTGGCGGAGTTCCTTTGCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtagataagttgaagtattttaacgttttcatatgtggaaatgaagtggtttttagaaaatgttttaatatgtatttt---catggttatgtatgtag

upper sequence: GRMZM2G178102_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 5'ss of exon 4

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtacttgtttttctagatagtgtgctaccctaatatggtgatgcacctgatgttgatatctctgaccgtttcaaacgtgatactgat-tgcag
||||||||| || |||||||||||  ||||||||||| |||||||||| ||||||||||||||| ||||||| || ||| ||||||||||||||   | ||  ||   ||   |  |    ||   | |   | || |  ||||  ||| |   |  |  |  ||  | | | |   | |    || ||
TCTACTCGCAATAGCTGAGGAGACCCTGGCAGAGTTCCTGTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAGgtacaat-ctctttcagcttcct--ttctttaatttcaccagttgctttacct--tgtagcagttcccaaatgtaaccatcttttgatttccatgtag

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|149071186|gb|EE159583.2|EE159583

EST:     CCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG                         CCTGGTCCGGATTCCGT
genomic: CCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtact ... ctgattgcagCCTGGTCCGGATTCCGT

EST: gi|148960630|gb|EE011258.2|EE011258

EST:     CCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG                         CCTGGTCCGGATTCCGTTGGAATCATCGCTGTTTCGCACAACTGCAGCGGC
genomic: CCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtact ... ctgattgcagCCTGGTCCGGATTCCGTTGGAATCATCGCTGTTTCGCACAACTGCAGCGGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 242

TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAGgtaatgtact ... ctgattgcagCCTGGTCCGGATTCCGTTGGAATCATCGCTGTTTCGCACAACTGCAGCGGCGTAGCAGCACGAGCTTGCGGCCTTGTGAGCCTTGAGCCCACAAAG

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 22

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 40