ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CTGGGTGTCTCTCTCGGGGTGCTCAACTGCTCACGCGTGGTTAATTTCTCGCTTTGGTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcag

Basic information

species	Zea mays
transcript	GRMZM2G157675_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g42090.1 (Oryza sativa), 5'ss of exon 1

CTGGGTGTCTCTCTCGGGGTGCTCAACTGCTCACGCGTGGTTAATTTC-TCGCTTTGGTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcag
   |   |||  || |    | | | || | |   || || |     | |||      |    ||||||||||||||||||||||||||||| ||||| |||||   |  | ||  |    |||| | |  || | ||     |||  || ||||| | ||||||||   ||   ||  | |     ||      |    | ||    |||    | | |||  |||||||
-CTGCCATCTAGCTAGCAAAGATGATCTCCCCGGACGCGGCTCGCAACGTCGTCGGCATCATCGGCAATGTCATCTCCTTCGGCCTCTTCCTCTCCCCCGTgtaactaagc-tctctaaacccggttgctgctagctg-----tttaattaatttgatgagggtttttggtgagatgtgagaactgaagaattaacaaatcttgatcttgt----ttgtgtgtgtgtgcag

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g42110.1 (Oryza sativa), 5'ss of exon 1

CTGGGTGTCTCTCTCGGGGTGCTCAACTGCTCACGCGTGGTTAATTTC-TCGCTTTGGTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcag
                      | | || | |   || || |     | |||      |    |||||||||||||||||||||||||||||  |||| |||||   |    |   ||    |  |   ||| |   |    | | | |     ||   ||| |    |        | | ||   ||    |    | |  ||  | | | |      |           
---------------------ATGATCTCCCCGGACGCGGCTCGCAACGTCGTCGGCATCATCGGCAATGTCATCTCCTTCGGCCTCTTCCTCGCCCCCGTgtaattaa--gttcttctaatcaagccgatc-gatcgaccatctctctctgcatg--caggataggatacaatacaacaaattctgaaattcatttctggttgtgtgtatatatgtatgcag--------

upper sequence: GRMZM2G157675_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os09g08490.1 (Oryza sativa), 5'ss of exon 1

CTGGGTGTCTCTCTCGGGGTGCTCAACTGCTCACGCGTGGTTAATTTCTCGCTTTG-GTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactcatcgatcggtccgggttcatctgggtggtttttttttttgatttggttagggttttgtttgtactgatatatggagaggcgcgccgccgcctgcatctgtgttctcgcgtgcctgtgcag
                             | |   | || |      |  | |  |  |    ||||||||||||||||| ||||||||||| || || |||    |||     |   | ||       ||  ||  |        ||       |   ||    | |      ||| |  || |   |                                          
----------------------ATGGTGTCCCggacttgatccgcaacgtggtgggcatcgtcggcaatgtcatctcctttggcctcttcctctcgccggtgcc--caccttctggcggatcatcaagaataaggacgtgcgggacttcaaggcggaccagtacctagcc-acgctgctcaattgcatgctctag------------------------------------

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|28188247|gb|CB179857.1|CB179857

EST:     GGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC

EST: gi|38229508|gb|CF919821.1|CF919821

EST:     GCTTTGGTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC
genomic: GCTTTGGTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC

EST: gi|28188031|gb|CB179641.1|CB179641

EST:     GGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGT                         GCTGCCGTTCTGGCGGATCTACAAGGCCAAGGACGCGGAGGAGTTCAAGCC
genomic: GGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCC

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 3 RNA-Seq libraries.

Block sizes: 37 (upstream exon), 49 (downstream exon)
Score: 4

CTGGGTGTCTCTCTCGGGGTGCTCAACTGCTCACGCGTGGTTAATTTCTCGCTTTGGTTTCAGGCAATGTCATCTCCTTCGGCCTCTTCCTGTCCCCAGTgtaggcactc ... gcctgtgcagGCTGACGTTCTGGCGGATCTACAAGGCCAAGGACGTGGAGGAGTTCAAGCCGGACCCTTACCTGGCGACGCTGCTCAACTGCATGCTCTGGGTGTTCTAT

Block sizes: 37 (upstream exon), 13 (downstream exon)
Score: 2