ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagggagctgttctttctgaaaactacattcccgttagattacatcaacattgctagtaaatgatgtcatttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG

Basic information

species	Zea mays
transcript	GRMZM2G154165_T04
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 16

--------gtaagggagctgttctttctgaaaactacattcccgttagattac-atcaacattgctagtaaatgat-----------gtcatttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG
         | |      | ||||||||||| | ||    ||  | |   |||  |  |  ||   | ||| |               ||  |  || || | ||| |||| ||||| || |||||||| |||||||| ||||| ||||| |||||||| | ||||||||||||  ||||||||||||| |||||  | |
ttcctatattgattttttttttctttctgaacaataatgccctttcatgctactgtgtatgttataaataagttcctcactatcttgatctctcatgtagGTTCATAGTGTATGGGCAGCAGCAGAAGCTTATTCAGCCCCTTCTATTGTTCTAACATCACATTCACATGATGGACTTCATGTTTTTGACGATTTTAGAG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 16

-------gtaagggagctgttctttctgaaaactacattcccgttagattac-atcaacattgctagtaaatgatgtcatttt------------tgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG
       |        || ||||||||||| | ||    ||  | |   |||  |  |  ||  ||  |||     ||| | |            || || | ||  |||| ||||| || ||||||||||||||||| ||||| ||||| |||||||| | ||||||||||||  ||||||| |||||||||||  | |
ttatattgattcttttcttttctttctgaacaataatgccctttcatgctactgtgtatgttaataacaaagttcctcactatcttgatctctcatgtagGTTCACAGTGTATGGGCAGCAGCAGAAGCATATTCAGCCCCTTCTATTGTTCTAACATCGCATTCACATGATGGAATTCATGTATTTGATGATTTTAGAG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 14
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 16

-----------gtaagggagctgttctttctgaaaactacattc--ccgttagatta--catcaacatt-----gctagta------aatg-atgtcatt--tttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG
            |    ||| |||| |||       | |  ||   | ||||| ||   | ||||||||     | ||| |      |||| ||  | ||  |||| ||||||||||||| ||||| |||||||||||||||||||| || ||||| ||  | |||||||  |||| ||||||  | || || |||||||||||  | |
gtatgcagactttcttcgagttgttattttatggtcccatcttttacagttagttttgtcgtcaacattcaaatgataggagttcgaaatgcatacctttgttttgtagATCCATTGTGTTTGGGCAGCTGCAGAAGCATATTCAGCTCCATCAATAGTTTTGACATCTCAGTCACGTGATGGCCTACACGTCTTTGATGATTTTAGAG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 14
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 16

-------------------gtaagggagctgttctttctgaaaactacattcccgtt-agattacatcaacattgctagtaaatgatgtcatttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG
                    |          || || |||  ||||  | | | ||| |||  | |  |    |   |||  | |   |  || ||| || | |||||||| ||||| ||||| ||||| || ||||| ||||| |||||  ||||||||| ||| ||||||||  |||| ||||||||||||||  | |
cctagcttggttctattccttctatttttcttttttcctgctaactgaaattctgttcagacaaaaaaagtcatttgagtgtaagtgatacttcttgtagGTTCATTGTGTTTGGGCAGCTGCGGAAGCTTACTCAGCCCCTTCTATTGTTTTAACATCTCATTCTCATGATGGCCTTCACGTTTTTGATGATTTTAGAG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 14
lower sequence: PP1S404_37V6.1 (Physcomitrella patens), 3'ss of exon 16

------------gtaagggagctgttctttctgaaaactacattcccgttaga-ttacat----caacattgctagtaaatgatgtca----tttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG
            | || | |  ||  ||| | |||| |    |     |   | || ||     | || | | |     ||| ||| |    |   ||||| | ||||||||||||||||| ||||| || || |||||||||||||||||||| ||||||||  |  | |||||  | || || ||||| |||||| | |
tgtctatgtggcgcaatgaatatgccctt-cagaaagccgggtcgtactcgaagttgcagagtacgacgtggatgacttatgttgttaaaattggctgcagGTTCATTGTGTGTGGGCTGCAGCAGAGGCTTACTCAGCACCTTCAATTGTGCTGACATCTCGGACTGAGGATGGAGTGCACGTCTTTGACGATTTCAGAG

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|33093933|gb|CF053927.1|CF053927

EST:     CATCTGCTGTGGGCATAATGCTGCTGACCATACTTTCTGGTTTTTACGTG                         ATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTT
genomic: CATCTGCTGTGGGCATAATGCTGCTGACCATACTTTCTGGTTTTTACGTGgtaagggagc ... atttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTG

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), 47 (downstream exon)
Score: 199

ACCTGTTGATCATAGAACCGAAGAAAAGCTTTTAGTACTGCCTTGTGGGCCATCTGCTGTGGGCATAATGCTGCTGACCATACTTTCTGGTTTTTACGTGgtaagggagc ... atttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG

Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 34

Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 15

Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 104

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctacattcccgttagattacatcaacattgctagtaaatgatgtcatttttgcagATCCATTGTGTGTGGGCTGCTGCAGAAGCATATTCAGCACCTTCAATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCG